Transcript November 8

Writing
Be concise!
What makes a good writer?
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Inborn talent?
Years of English and humanities classes?
An artistic nature?
The influence of alcohol and drugs?
Divine inspiration?
•Having something to say
•Logical and clear thinking
•Knowing a few simple, learnable rules of style
Clear writing starts with clear thinking
Before you start writing, ask:
“What am I trying to say?”
When you finish writing, ask:
“Have I said it?”
Make every word tell
“Vigorous writing is concise. A sentence
should contain no unnecessary words, a
paragraph no unnecessary sentences, for
the same reason that a drawing should
have no unnecessary lines and a machine
no unnecessary parts. This requires not
that the writer make all his sentences
short, or that he avoid all detail and treat
his subjects only in outline, but that every
word tell.”
The Elements of Style, William Strunk Jr.
(available online at: http://www.bartleby.com/141/)
Make every word tell
“Such preparations shall be made as will
completely obscure all Federal buildings and
non-Federal buildings occupied by the
Federal government during an air raid for any
period of time from visibility by reason of
internal or external illumination.”
(from a US government blackout order in 1942)
FDR’s response:
“Tell them that in the buildings where they
have to keep the work going to put
something across the windows.”
Words and sentences
Words
1. Reduce dead weight
2. Cut, cut, cut
3. Be specific
Sentences
4. Include subject + verb + object
5. Use strong verbs
6. Eliminate negatives; use positive constructions
Dead weight
• Very, really, quite, basically, generally
• Watch out for the verb “to be” (e.g., “there are”)
There are many students who like writing.
Many students like writing
Dead weight
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In the event that
In the nature of
It has been estimated that
It seems that
It may be argued that
It can be shown that
It is believed that
For the most part
For the purpose of
In the case of
In the final analysis
Dead weight
Clunky phrase
Equivalent
• A majority of
Most
• A number of
Many
• Are of the same opinion
Agree
• At the present moment
Now
• By means of
By
Dead weight
Clunky phrase
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All three of the
Fewer in number
Give rise to
In all cases
In a position to
In close proximity to
In order to
Equivalent
The three
Fewer
Cause
Always
Can
Near
To
Dead weight
Beware of
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Assistance
Utilize
Numerous
Facilitate
Remainder
Due to the fact that
Is indicative of
Sufficient
For the purpose of
Use instead
Help
Use
Many
Help
Rest
Because
Shows
Enough
For/to
Choosing the right words
1.
2.
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Reduce dead weight words and phrases
Cut, cut, cut
Is a word or phrase necessary?
What happens if I take it out?
Don’t get attached!
Cutting words
I would like to assert that the author should be considered
to be a buffoon.
The author is a buffoon.
The expected prevalence of mental retardation, based on the
assumption of a normal distribution of intelligence in the
population, is stated to be theoretically about 2.5%.”
The expected prevalence of mental
retardation, if intelligence is normally
distributed, is 2.5%
Cutting words
To control infection with Mycobacterium tuberculosis (M.
tb), a robust T-cell-mediated immune response is
necessary, and deficiency in this response predisposes an
individual towards active TB.
Deficiency in T-cell-mediated immune response
predisposes an individual to active TB.
Cutting words
This paper provides a reviewS of the basic tenets of
cancer biology study design, using as examples studies
that illustrate the methodologic challenges and
or that
demonstrate successful solutions to the difficulties
inherent in biological research.
This paper reviews cancer biology study design, using
examples that illustrate specific challenges and solutions.
Choosing the right words
1. Reduce dead weight words and phrases
2. Cut, cut, cut: learn to part with your
words
3. Be specific
Use specific nouns and specific verbs and specific
details….
Be specific
Vague nouns
Problem, situation, approach, method, reaction, period,
component, technique, solution, challenge, difficulty
Vague: A period of unfavorable weather set in.
Specific: It rained every day for a week.
Building sentences
Sentences
4. Subject + verb + object
5. Use strong verbs and don’t turn verbs
into nouns
6. Eliminate negatives; use positive
constructions
Active vs. passive voice
In the passive voice, the actor is AWOL…
President Kennedy was shot in 1963.
Who shot him?
Cigarette ads were designed to appeal to children.
Who is responsible?
Building sentences
4. Subject + verb + object
5. Use strong verbs and don’t turn verbs
into nouns
Active verbs
Weak verbs
Obtain estimates of
estimate
Has seen an expansion in
has expanded
Provides a methodologic emphasis emphasizes
Take an assessment of
The useful bits
assess
More active verbs
Provide a review of
review
Offer confirmation of
confirm
Make a decision
decide
Shows a peak
peaks
Exhibits a dependence upon
depends
Building sentences
4. Subject + verb + object
5. Use strong verbs and don’t turn verbs into
nouns
6. Eliminate negatives; use positive constructions
Be positive
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Not honest
Does not have
Did not remember
Did not pay attention to
Did not have much confidence
Did not succeed
dishonest
lacks
forgot
ignored
distrusted
failed
Example
Subject very long!
The fear expressed by some teachers that
students would not learn statistics well if they
were permitted to use canned computer Negatives
programs has not been realized in our
Passive
experience. A careful monitoring of achievement
Dead weight
levels before and after the introduction of
computers in the teaching of our course
revealed no appreciable change in students’
performances.
Boring verb
55 words
Example
Many teachers feared that the use of canned
computer programs would prevent students
from learning statistics. We monitored student
achievement levels before and after the
introduction of computers in our course and
found no decrease in performance.
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Dangling participles
& misplaced modifiers
Participles modify the nearest noun
Walking along the beach, the sun rose majestically over the ocean.
Using tissue isolation protocol, mtDNA was isolated from dried
skins.
Ivory samples were taken from tusks using a drill.
Paragraphs
1. Avoid a succession of loose sentences
2. Paragraph flow is helped by:
• logical flow of ideas
• if necessary, transition words
3. First and last sentences should be really good
Abstract
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Summary of research
At beginning of paper (write last!)
Conference proceedings
Short! (150-250 words)
Give max information in min space
Weissman 2008
Abstract structure
• Purpose (1-2 sentences)
• Procedures (very abbreviated)
• Findings
• Conclusions (1-2 sentences of discussion;
1 sentence about general importance)
Mori et al. Circadian clock protein KaiC forms ATP-dependent
hexameric rings and binds DNA. PNAS 99: 17203-17208
KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential
circadian clock protein in cyanobacteria. Previous sequence analyses
suggested its inclusion in the RecA/DnaB superfamily. A characteristic of
the proteins of this superfamily is that they form homohexameric
complexes that bind DNA. We show here that KaiC also forms ring
complexes with a central pore that can be visualized by electron
microscopy. A combination of analytical ultracentrifugation and
chromatographic analyses demonstrates that these complexes are
hexameric. The association of KaiC molecules into hexamers depends
on the presence of ATP. The KaiC sequence does not include the
obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless,
KaiC binds forked DNA substrates. These data support the inclusion of
KaiC into the RecA/DnaB superfamily and have important implications
for enzymatic activity of KaiC in these circadian clock mechanism that
regulates global changes in gene expression patterns.
143 words
Mori et al. Circadian clock protein KaiC forms ATP-dependent
hexameric rings and binds DNA. PNAS 99: 17203-17208
KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential
circadian clock protein in cyanobacteria. Previous sequence analyses
suggested its inclusion in the RecA/DnaB superfamily. A characteristic of
the proteins of this superfamily is that they form homohexameric
complexes that bind DNA. We show here that KaiC also forms ring
complexes with a central pore that can be visualized by electron
microscopy. A combination of analytical ultracentrifugation and
chromatographic analyses demonstrates that these complexes are
hexameric. The association of KaiC molecules into hexamers depends
on the presence of ATP. The KaiC sequence does not include the
obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless,
KaiC binds forked DNA substrates. These data support the inclusion of
KaiC into the RecA/DnaB superfamily and have important implications
for enzymatic activity of KaiC in these circadian clock mechanism that
regulates global changes in gene expression patterns.
143 words
Mori et al. Circadian clock protein KaiC forms ATP-dependent
hexameric rings and binds DNA. PNAS 99: 17203-17208
KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential
circadian clock protein in cyanobacteria. Previous sequence analyses
suggested its inclusion in the RecA/DnaB superfamily. A characteristic of
the proteins of this superfamily is that they form homohexameric
complexes that bind DNA. We show here that KaiC also forms ring
complexes with a central pore that can be visualized by electron
microscopy. A combination of analytical ultracentrifugation and
chromatographic analyses demonstrates that these complexes are
hexameric. The association of KaiC molecules into hexamers depends
on the presence of ATP. The KaiC sequence does not include the
obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless,
KaiC binds forked DNA substrates. These data support the inclusion of
KaiC into the RecA/DnaB superfamily and have important implications
for enzymatic activity of KaiC in these circadian clock mechanism that
regulates global changes in gene expression patterns.
143 words
Mori et al. Circadian clock protein KaiC forms ATP-dependent
hexameric rings and binds DNA. PNAS 99: 17203-17208
KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential
circadian clock protein in cyanobacteria. Previous sequence analyses
suggested its inclusion in the RecA/DnaB superfamily. A characteristic of
the proteins of this superfamily is that they form homohexameric
complexes that bind DNA. We show here that KaiC also forms ring
complexes with a central pore that can be visualized by electron
microscopy. A combination of analytical ultracentrifugation and
chromatographic analyses demonstrates that these complexes are
hexameric. The association of KaiC molecules into hexamers depends
on the presence of ATP. The KaiC sequence does not include the
obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless,
KaiC binds forked DNA substrates. These data support the inclusion of
KaiC into the RecA/DnaB superfamily and have important implications
for enzymatic activity of KaiC in these circadian clock mechanism that
regulates global changes in gene expression patterns.
143 words
Mori et al. Circadian clock protein KaiC forms ATP-dependent
hexameric rings and binds DNA. PNAS 99: 17203-17208
KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential
circadian clock protein in cyanobacteria. Previous sequence analyses
suggested its inclusion in the RecA/DnaB superfamily. A characteristic of
the proteins of this superfamily is that they form homohexameric
complexes that bind DNA. We show here that KaiC also forms ring
complexes with a central pore that can be visualized by electron
microscopy. A combination of analytical ultracentrifugation and
chromatographic analyses demonstrates that these complexes are
hexameric. The association of KaiC molecules into hexamers depends
on the presence of ATP. The KaiC sequence does not include the
obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless,
KaiC binds forked DNA substrates. These data support the inclusion of
KaiC into the RecA/DnaB superfamily and have important implications
for enzymatic activity of KaiC in these circadian clock mechanism that
regulates global changes in gene expression patterns.
143 words
Assignment
• Write an abstract of paper provided
• Max: 150 words
• Due: Monday, November 15 (by email)
Introductions
BIG picture
General background,
i.e., what is known
The gap: what is
not known
Your question/
goals
Your
approach
Introduction structure
Martínez-González et al. (2008) Adherence to Mediterranean diet and
risk of developing diabetes: prospective cohort study. BMJ
First paragraph: What is known about risk factors for diabetes
Diabetes mellitus is an increasingly important global public health problem
that threatens to reach pandemic levels by 2030.As some randomised trials
have consistently shown, increased physical activity and weight loss are
efficient approaches for the control and prevention of type 2 diabetes. Diet
has also long been believed to be an important risk factor for diabetes.
Second paragraph: What is known about the Mediterranean
diet and diabetes
Many studies have shown that the Mediterranean food pattern has a
role in prevention of cardiovascular disease.The similarity of some risk
factors and some empirical and mechanistic evidence suggest that the
Mediterranean diet can also protect against diabetes. The major
protective characteristics include a high intake of fibre, a high intake of
vegetable fat, a low intake of trans fatty acids, and a moderate intake of
alcohol. Moreover, a particular feature of the diet is the abundant use of
virgin olive oil for cooking, frying, spreading on bread, or dressing
salads.This leads to a high ratio of monounsaturated fatty acids to
saturated fatty acids. This ratio can be used to score adherence to a
Mediterranean diet as the traditional diet. Despite having a relatively
high total fat content, this food pattern is rich in monounsaturated fatty
acids (from olive oil) and poor in saturated fatty acids. Diets rich in
monounsaturated fatty acids improve lipid profiles and glycaemic
control in people with diabetes, suggesting that a high intake improves
insulin sensitivity.Together these associations suggest the hypothesis
that following an overall pattern of Mediterranean diet can protect
against diabetes. In addition to having a long tradition of use without
evidence of harm, a Mediterranean diet is highly palatable, and people
are likely to comply with it.
Third paragraph : What is not known about the Mediterranean
diet and diabetes
Few prospective studies have evaluated the specific role of the
Mediterranean diet on the risk of developing diabetes in initially healthy
Mediterranean populations. A prospective follow-up study recently reported
an inverse association between adherence to the diet and the incidence of
diabetes. All members of that study, however, had survived a previous
myocardial infarction and the tool to assess dietary habits had inherent
limitations because it included only a short list of items, and the authors did
not attempt to measure the entire diet.
Fourth paragraph : What this study did and why it’s better than
previous studies
We evaluated the association between adherence to a Mediterranean diet
and the incidence of diabetes using a full validated food frequency
questionnaire to measure the entire diet.
Plagiarism of structure = bad
Point B
Point A
Point C
Point D
Emulation = good
Model/ system
Problem
Question
Your approach
Assignment
• Write a 1-1.5 page Introduction for a NSERC
Discovery Grant
• single-spaced, 12 pt font, with 2.5 cm margins
• Use two major headings: (1) Objectives and (2)
Background. You may also use subheadings
within these major headings.
• Include references (not included in the space
limit).
• Due: Monday, November 22 (by email, as Word
document)