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Genome 547- Scientific Writing
All are agreed that the articles in our journals-even the journals with the highest
possible standards-are, by and large, poorly written. Some of the worst are
produced by the kind of author who consciously pretends to a ‘scientific
scholarly’ style.
[Many students begin graduate school with good writing skills]… Two years [into
graduate school] these same students’ writing is verbose, pompous, full of
fashionable circumlocutions… The student can no longer write, he pontificates.
What has brought about the change? Clearly the students have copied these
dreary and pretentious phrases from the scientific literature. They have been
dutifully studying it as they are urged to do, and it has warped their style to the
point that they can no longer walk to the door without “utilizing a pedestrian
relocation,” or sip their coffee without “prior elevation of the containing vessel to
facilitate imbibation.”
F. Peter Woodford, Editor of Science.
1. Manuscript Organization (Robert A. Day, J.R. Matthews & Stan Fields)
A. TITLE
Adequately describes the paper in the fewest possible words.
In general, you should avoid using abbreviations and jargon.
Article titles have evolved from statements declaring the nature of the study (e.g., “Molecular
Structure of Nucleic Acids,” “Mutations of bacteria from virus sensitivity to virus
resistance”) to statements declaring the results of the study (“Apoptosis Initiated When BH3
Ligands Engage Multiple Bcl-2 Homologs, Not Bax or Bak” (current issue of Science),
“Kinetochore Orientation during Meiosis Is Controlled by Aurora B and the Monopolin
Complex” (current issue of Cell)).
Which style you prefer to follow is a matter of personal preference.
B. ABSTRACT
Provides a brief (often 250 words or less) summary of each of the main sections of the paper:
Introduction, Materials and Methods, Results, and Discussion. Do not include information that
is not stated in other parts of the manuscript.
The abstract is probably the most important part of the manuscript because many people will
read this and neglect the rest of the paper.
C. INTRODUCTION
Supplies sufficient background information to allow the reader to understand and evaluate the
results of the present study without needing to refer to previous publications on the topic.
Provides rationale for the present study: What is the purpose of this paper?
Some rules for a good introduction:
1.
Present the nature and scope of the problem investigated; why is the
problem important?
2.
Review the pertinent literature to orient the reader.
3.
State the method of the investigation; if necessary, the reasons for the
choice of method.
4.
State the principle results of the investigation.
5.
State the principle conclusions.
Release of neurotransmitter from chemical synapses is the primary method of
communication between neurons, and the regulation of this process is crucial for
plastic changes within the nervous system.
VAMP or synaptobrevin, syntaxin, and SNAP-25 bind to each other in vitro in a
complex that is thought to be at the heart of vesicle docking and fusion.
C. INTRODUCTION
Supplies sufficient background information to allow the reader to understand and evaluate the
results of the present study without needing to refer to previous publications on the topic.
Provides rationale for the present study: What is the purpose of this paper?
Some rules for a good introduction:
1.
Present the nature and scope of the problem investigated; why is the
problem important?
2.
Review the pertinent literature to orient the reader.
3.
State the method of the investigation; if necessary, the reasons for the
choice of method.
4.
State the principle results of the investigation.
5.
State the principle conclusions.
Release of neurotransmitter from chemical synapses is the primary method of
communication between neurons, and the regulation of this process is crucial for
plastic changes within the nervous system.
DiAntonio, A. (1993) Cell 73, 1281.
VAMP or synaptobrevin, syntaxin, and SNAP-25 bind to each other in vitro in a
complex that is thought to be at the heart of vesicle docking and fusion.
Deitcher, DL. (1998) J. Neurosci. 18, 2028.
D. MATERIALS AND METHODS
Describe the experimental design and provide enough detail so that the experiment can be
repeated.
For Materials, include exact technical specifications and quantities and source of method of
preparation.
Identify animals, plants, and microorganisms accurately, usually by genus, species and strain
designation.
For methods, the usual order of presentation is chronological; however, related methods
should be described together.
Be precise in measurements, e.g., precise temperature, quantity, time, etc.
If a method has been published, only the literature reference need be given, although it is
useful to identify the method briefly. For example, “cells were broken by ultrasonic treatment
as previously described (9),” rather than, “cells were broken as previously described (9).”
When large numbers of strains, mutants or chemicals are used, prepare tables identifying
source and properties.
Do not include results in the Materials and Methods section.
E. RESULTS
One of the easiest parts of a manuscript to write (and often a good place to begin your writing).
Begin (usually) by providing a big-picture description of the experiments, then present the data.
Results should be in the past tense.
Present representative data, rather than endlessly repetitive data.
If there are only one or a few determinations, present them descriptively in the text. For
multiple determinations, use a figure (graph) or table.
Do not present identical data in the text and in the figures and tables.
The paper stands or falls on the basis of the results.
F. DISCUSSION
Often the hardest part of a manuscript to write. Many are too long and verbose.
Essential features:
1.
Present the principles, relationships and generalizations shown by the
Results. Discuss, but do not recapitulate the Results.
2.
Point out exceptions or lack of correlation and define unsettled points. Don’t
try to cover up or fudge data that don’t fit.
3.
Show how results and interpretations agree or contrast with previous
publications.
4.
Discuss theoretical implications, or practical applications.
5.
State conclusions as clearly as possible.
6.
Summarize evidence for each conclusion.
Reference to current work or findings traditionally uses the past tense (e.g., “we showed”). Use
of present tense (e.g., “We show”) has become popular with the advent of “glamour journals”
such as Cell, Science, etc., and is now common. Which style you prefer to follow is a matter of
personal preference.
G. TABLES/GRAPHS
Tables and figures should both stand alone and be an indispensable part of the text. Readers
should be able to understand figures without referring to the text; ideally figures should be
understandable without reading the figure legend.
Raychaudhuri, S. et al.,(2006) J. Cell Biol 173, 107–119.
Figure 7. Osh proteins are not required for PS transport
to mitochondria and the Golgi complex. (A–G) Strains were
labeled with 3H-serine at nonpermissive temperature as described
in Materials and methods. Lipids were extracted and
the amounts of radiolabeled PS, PE, and PC were determined.
The percent of the total of these three lipids was calculated.
Values are the mean of at least three determinations. Error bars
indicate the SEM. n = 3.
Raychaudhuri, S. et al.,(2006) J. Cell Biol 173, 107–119.
If data show pronounced trends or make an interesting picture, use a graph. If numbers show
no exciting trend, or you need to present exact numbers, use a table.
Some additional guidelines:
Exact values, raw data, or data that do not
fit into any simple pattern
Summarize trends, relate data to
constants, emphsize overa ll pattern rather
than spec ific measurement
Draw comparisons
Illustrate complex relationships, spatial
configurations, pathways, processes,
interact ions
Sequential processes
Describe proportions
Table, list
Line graph
Bar graph
Diagram
Flowchart
Pie chart, bar graph
Readers can compare items down a column easier than across a row. Place independent variable in rows and
dependent variables in columns.
Determination
Optimal growth
temperature (ºC)
Color of mycelium
Antibiotic
Produced
Yield of antibiotic
(mg/ml)
S. fluoricolor
-10
S. griseus S. coelicolor
24
28
S. nocolor
92
Tan
flurocillinmycin
grey
streptomycin
red
rholmondelay
purple
neomycin
4,108
78
2
0
vs.
Organism
S. fluoricolor
S. griseus
S. coelicolor
S. nocolor
Optimal growth
temperature (ºC)
-10
24
28
92
Color of
mycelium
tan
grey
red
purple
Antibiotic
produced
flurocillinmycin
streptomycin
rholmondelay
neomycin
Yield of antibiotic
(mg/ml)
4,108
78
2
0
2. Basic Definitions of Grammatical Terms
(http://www.colorado.edu/slhs/CLL/latindef.htm &
http://www.ucalgary.ca/UofC/eduweb/grammar/)
A. PARTS OF SPEECH
NOUN -- A noun is a naming word, a word that identifies a person, place, thing, or abstract
idea.
The name of a specific person or place--such as Jane Doe, Abraham Lincoln, New York, or
England--is called a proper noun.
A few common nouns: house, boss, dogs, football, mother, kitchen, King George, beauty,
desks, crime, nation, boy, tempest, tea, coffee. (if you can put "a", "an", or "the" in front of a
word and have it mean something, it is a noun.)
PRONOUN -- Pronouns are words that take the place of nouns. I, you, he, she, it, they, this,
that, who, which are all pronouns. The most common pronouns are words like "them", him,
her, he, she.
VERB -- The verb is a part of speech, a word or compound of words, that performs one of
three kinds of tasks: it expresses action; it expresses a state of being; or it expresses the
relationship between two things. In its most powerful and normal position, it follows a noun (the
agent of the verb).
A few verbs: is, are, am, was, were (all versions of the verb "to be"), jump, sing, kick, use,
decide, resemble, play, explode, encounter, celebrate, hope, say, decide, leap, attack,
announce, cook.
ADJECTIVE -- An adjective describes, or modifies, a noun.
A few adjectives: rich, fat, green, sixty thousand, amazing, purple, unidentified, happy, tired,
asleep, four, Roman, modern, clear, uncertain.
ADVERB -- First, an adverb describes, or modifies, a verb. It tells something about how or
when the verb was done.
A few adverbs: happily, well, later, tomorrow, soon, quickly, never, perfectly, slowly, badly, now,
then, quietly, loudly, slowly, sadly.
Second, an adverb can modify (tell about) an adjective: the perfectly clear sky, extremely good
food, terribly loud noise, beautifully green eyes. (adverbs are often formed with -ly at the end.)
Third, an adverb can modify another adverb: She sings well, very well. He jumped
far, amazingly far. They left soon, too soon.
B. SENTENCE ELEMENTS
SUBJECT -- The subject of a sentence is the noun or pronoun (person or thing) about which
an assertion is made or a question is asked. The subject is the person or thing that the
sentence is mainly about. Subjects can either be “simple” (composed of a single noun or
pronoun) or “complex.”
Examples:
The man who had followed us inside walked over to the telephone.
The superior performance of La Traviata pleased the wealthy audience.
Simple subject
Complex subject
DIRECT OBJECT -- The direct object receives the action of the verb. Some students have
called the direct object "the victim of the verb".
My friends invited me and my room-mate. We accepted the invitation. We all drank beer
and watched videos.
In most sentences the word order pattern is: {Subject}, {verb}, {direct object}.
PREPOSITION -- A preposition comes before (pre) a noun or pronoun, and shows the
relationship (-position) of that person or thing to something else.
A few prepositions: in, into, on, onto, over, under, through, to, up, down, by, with, from, of, out,
between, across, without, for.
3. Characters and Actions (Joseph M. Williams & Robert A. Day)
Once upon a time, as a walk through the woods was taking place on the part of little red riding
hood, the wolf’s jump out from behind a tree occurred, causing her fright.
Once upon a time, little red riding hood was walking through the woods, when the wolf jumped
out from behind a tree and frightened her.
DIRECT OBJECT -- The direct object receives the action of the verb. Some students have
called the direct object "the victim of the verb".
My friends invited me and my room-mate. We accepted the invitation. We all drank beer
and watched videos.
In most sentences the word order pattern is: {Subject}, {verb}, {direct object}.
PREPOSITION -- A preposition comes before (pre) a noun or pronoun, and shows the
relationship (-position) of that person or thing to something else.
A few prepositions: in, into, on, onto, over, under, through, to, up, down, by, with, from, of, out,
between, across, without, for.
3. Characters and Actions (Joseph M. Williams & Robert A. Day)
Once upon a time, as a walk through the woods WAS TAKING PLACE on the part of little red
riding hood, the wolf’s jump out from behind a tree OCCURRED, causing her fright.
Once upon a time, little red riding hood WAS WALKING through the woods, when the wolf
JUMPED out from behind a tree and frightened her.
simple subjects
main characters
VERBS
DIRECT OBJECT -- The direct object receives the action of the verb. Some students have
called the direct object "the victim of the verb".
My friends invited me and my room-mate. We accepted the invitation. We all drank beer
and watched videos.
In most sentences the word order pattern is: {Subject}, {verb}, {direct object}.
PREPOSITION -- A preposition comes before (pre) a noun or pronoun, and shows the
relationship (-position) of that person or thing to something else.
A few prepositions: in, into, on, onto, over, under, through, to, up, down, by, with, from, of, out,
between, across, without, for.
3. Characters and Actions (Joseph M. Williams & Robert A. Day)
Once upon a time, as a walk through the woods WAS TAKING PLACE on the part of little red
riding hood, the wolf’s jump out from behind a tree OCCURRED, causing her fright.
Once upon a time, little red riding hood WAS WALKING through the woods, when the wolf
JUMPED out from behind a tree and frightened her.
simple subjects
main characters
VERBS
 In a clear sentence, the main characters are subjects and verbs name the actions of the
characters.
The federalists’ argument in regard to the destabilization of government by popular democracy
was based on their belief in the tendency of factions to further their self-interest at the expense
of the common good.
Simple subject?
Main characters?
Verbs?
Actions?
The federalists’ argument in regard to the destabilization of government by popular democracy
was based on their belief in the tendency of factions to further their self-interest at the expense
of the common good.
Simple subject? argument
Main characters?
Verbs?
Actions?
The federalists’ argument in regard to the destabilization of government by popular democracy
was based on their belief in the tendency of factions to further their self-interest at the expense
of the common good.
Simple subject? argument
Main characters? federalists, government, popular democracy, factions
Verbs?
Actions?
The federalists’ argument in regard to the destabilization of government by popular democracy
was based on their belief in the tendency of factions to further their self-interest at the expense
of the common good.
Simple subject? argument
Main characters? federalists, government, popular democracy, factions
Verbs? was based, further
Actions?
The federalists’ argument in regard to the destabilization of government by popular democracy
was based on their belief in the tendency of factions to further their self-interest at the expense
of the common good.
Simple subject? argument
Main characters? federalists, government, popular democracy, factions
Verbs? was based, further
Actions? argue, destabilize, believe, further
The federalists’ argument in regard to the destabilization of government by popular democracy
was based on their belief in the tendency of factions to further their self-interest at the expense
of the common good.
Simple subject? argument
Main characters? federalists, government, popular democracy, factions
Verbs? was based, further
Actions? argue, destabilize, believe, further
Rewriting to make the main characters subjects and the actions verbs yields:
The federalists ARGUED that popular democracy DESTABILIZED government, because
they BELIEVED that factions TENDED to FURTHER their self-interest at the expense of the
common good.
simple subjects
main characters
VERBS
Abstractions as characters
Readers prefer that subjects of verbs be flesh-and-blood characters. When you write about
concepts, however, you can turn them into virtual characters by making them the subjects of
verbs that communicate actions:
No right is more fundamental to a free society than freedom of speech. Free speech served
the left in the 1960’s when it protested the Vietnam war; and it is now used by the right when it
claims that speech includes political contributions. The doctrine of free speech has been
embraced by all sides to protect themselves against those who would silence unpopular views.
As a legal concept, it arose….
Alternatively, you can describe unfamiliar abstractions from the point of view of flesh-and-blood
characters:
I argue this about intention. It has a complex cognitive component of two temporal kinds:
prospective intention and immediate intention. Prospective intention lets us represent how we
have acted in the past and in our present situation, and how we will act in the future. That is,
we use the cognitive component of prospective intention to help us plan. Immediate intention
lets us monitor and guide our bodies as we move them…
Nominalizations
Writing seems dense when abstract nouns derived from verbs and adjectives (nominalizations)
are used frequently, especially when those nouns are subjects of verbs.
Nominalizations are nouns ending in –tion, -ment, -ence, etc.
gerunds (verbs ending in -ing) can also act as nominalizations.
Examples:
Verb  Nominalization
Discover  discovery
Resist  resistance
react  reaction
utilize, use  Utilization
reduce  reduction
Adjective  Nominalization
careless  carelessness
different  difference
proficient  proficiency
know  knowledge
Try to identify actions that are expressed as nominalizations and change them into verbs:
The intention of the committee is to audit the records.
Change to:
The committee intends to audit the records.
Why change nominalizations into verbs?
First, you generally eliminate prepositions in the process; second, you often eliminate “to be”
verbs by replacing them with action verbs; and third, you humanize the text by saying who
does what. Humanizing the text makes it less abstract and allows the readers to more easily
visualize what you are talking about. For example:
The data are indicative of the problem.  the data indicate the problem.
…is applicable  applies
…is deserving  deserves
…is in agreement  agrees
…is in error  errs
…is possessed of  possesses
How to spot problems in your own writing?
Look at the first seven or eight words in your sentences. If you don’t see in those words a
character as a subject and a verb as an action, that sentence is a candidate for revision.
 In a clear sentence, the main characters (flesh and blood or abstract) are subjects
and most of the verbs name the actions of the characters.
4. Active vs. Passive voice (Joseph M. Williams, Michael Alley &
http://www.ucalgary.ca/UofC/eduweb/grammar/))
The "voice" of a verb has to do with whether or not the subject of a sentence acts upon
something else (as agent) or whether the subject is acted upon (by an agent).
The verb is active, when the subject (agent) does the action (verb) to something (object). The
verb is passive, when the subject takes the action upon itself.
Examples:
Active
John ate the apples.
John, the subject, is the one performing the action of the verb.
Passive
The apples were eaten by John.
The apples, the subject in this sentence, are receiving the action of the verb.
Recognizing Passive Constructions
Step 1: Find any form of the verb "to be": is, was, were, will be, will have been, would be and
so on. Note that tense does not affect voice; passive can take any tense.
Step 2: Is that form of the verb "to be" followed by a past tense verb? (watched, threatened,
considered, thought, and so on.
Step 3: Does the word "by" appear after the whole verb or can you put the word "by" after the
combination of the "to be" verb and the past tense verb.
The passive voice in science writing
The passive voice is common in science writing, particularly in older papers. However, passive
voice verbs either delay the real subject or erase it completely. The passive verb also requires
more words than the active verb, has less impact than the active verb, and generally suggests
passivity, hesitancy, or a lack of clarity on the part of the writer.
By contrast, active voice foregrounds the real agent of the action, provides force and clarity in
one's statements, and avoids wordiness in sentence constructions. Active voice is
performative; passive is static, even though action and agency seem to exist in the sentence.
 The passive voice is used too much in science writing, but it does have its uses. Use it in
these circumstances:
-You want to focus your reader’s attention on one or another character:
On the second day of our wildebeest study, one of the calves wandered just a few yards from
the herd and was attacked by wild dogs. [emphasizes the wildebeest calve]
vs.
On the second day of our wildebeest study, wild dogs attacked one of the calves that
wandered just a few yards from the herd. [emphasizes the wild dogs]
-You want to shift a long and complex bundle of information to the end of a sentence,
especially when it also lets you move to its beginning information that is shorter and more
familiar. For example, compare the middle sentences in the following passages:
Some astonishing questions about the nature of the universe have been raised by scientists
studying black holes in space. The collapse of a dead star into a point perhaps no larger than
a marble creates a black hole. So much matter compressed into so little volume changes the
fabric of space around it in puzzling ways.
vs.
Some astonishing questions about the nature of the universe have been raised by scientists
studying black holes in space. A black hole is created by the collapse of a dead star into a
point perhaps no larger than a marble. So much matter compressed into so little volume
changes the fabric of space around it in puzzling ways.