This is an academic writing style guide written for programmers, compiled from Writing in the Sciences by Stanford University.
- Academic Writing Style Guide for Programmers
- Table of Contents
- 0. Introduction
- 1. Cut the clutter
- 1.1. Dead weight words and phrases
- 1.2. Empty words and phrases
- 1.3. Long words or phrases that could be short
- 1.4. Unnecessary jargon and acronyms
- 1.5. Repetitive words or phrases
- 1.6. Generic adverbs
- 1.7. Eliminate negatives
- 1.8. Eliminate superfluous uses of "there is/are"
- 1.9. Omit needless propositions
- 1.10 EXAMPLES
- 2. Use active voice
- 3. Paragraph editing
- 4. Writing Process
- 5. The original manuscript
- 6. Plagiarism
- 7. Further Reading
-
Good writing communicates an idea clearly and effectively. (Takes having something to say and clear thinking.)
-
Good writing is elegant and stylish. (Takes time, revision, and a good editor!)
-
Having something to day.
-
Logical thinking.
-
A few simple, learnable rules of style.
- Read, pay attention, and imitate.
- Let go of “academic” writing habits (deprogramming step!)
- Talk about your research before trying to write about it.
- Write to engage your readers—try not to bore them!
- Stop waiting for “inspiration.”
- Accept that writing is hard for everyone.
- Revise. Nobody gets it perfect on the first try.
- Learn how to cut ruthlessly. Never become too attached to your words.
-
Complex ideas don't require complex language.
-
Scientific writing should be easy and even enjoyable to read!
-
Cut unnecessary words and phrases; learn to part with your words!
-
Use the active voice (subject + verb + object).
-
Write with verbs: use strong verbs, avoid turning verbs into nouns, and don’t bury the main verb!
Dead weight words and phrases should be removed directly. Instead, give references.
For example,
As it is well known
As it has been shown
It can be regarded that
It should be emphasized that
should be replaced by references.
Empty words and phrases should be removed directly, because they convey no information.
For example,
basic tenets of
methodological
important
should be removed directly.
Long words or phrases can always be converted to short words.
| Wordy | Crisp |
|---|---|
| based on the assumption that | if |
| a majority of | most |
| a number of | many |
| give rise to | cause |
| have an effect on | affect |
Too many jargons/acronyms slow down the readers.
| Wrong | Right |
|---|---|
| miR | micro RNA |
Repetitive words or phrases should be compressed into a single word.
For example, only one word should be left for each of the following tuples:
studies/examples
illustrate/demonstrate
challenges/difficulties
successful solutions
Generic adverbs should never exist in the scientific paper.
For example,
very
really
quite
basically
generally
should be removed directly.
Negatives should be converted to positives.
| Wrong | Right |
|---|---|
| Not honest | dishonest |
| Not harmful | safe |
| Not important | unimportant |
| Does not have | lacks |
| Did not remember | forgot |
| Did not pay attention to | ignored |
| Did not succeed | failed |
All "There is/are" should be removed.
- Examples
There are many ways in which we can arrange the pulleys.
There was a long line of bacteria on the plate.
There are many physicists who like to write.
The data confirm that there is an association between vegetables and cancer.
should be replaced by
We can arrange the pulleys in many ways.
Bacteria lined the plate.
Many physicists like to write.
The data confirm an association between vegetables and cancer.
All needless propositions should be removed.
e.g. "on" and "that" are often superfluous.
- Examples
The meeting happened on Monday.
They agreed that it was true.
should be replaced by
The meeting happened Monday.
They agreed it was true.
Bad:
These findings imply that the rates of ascorbate radical production and its recycling via dehydroascorbate reductatse to replenish the ascorbate pool are equivalent at the lower irradiance, but not equivalent at higher irradiance with the rate of ascorbate radical production
exceeding its recycling back to ascorbate.
Better:
These findings imply that, at low irradiation, ascorbate radicals are
produced and recycled at the same rate, but at high irradiation, they are produced faster than they can be recycled back to ascorbate.
Bad:
Dysregulation of physiologic microRNA (miR) activity has been shown to play an important role in tumor initiation and progression, including gliomagenesis. Therefore, molecular species that can regulate miR activity on their target RNAs without affecting the expression of relevant mature miRs may play equally relevant roles in cancer
Better:
Changes in microRNA expression play a role in cancer, including glioma.
Therefore, events that disrupt microRNAs from binding to their target
RNAs may also promote cancer
Bad:
This paper provides a review of the basic tenets of cancer biology study design, using as examples studies that illustrate the methodologic challenges or that demonstrate successful solutions to the difficulties inherent in biological research.
Better:
This paper reviews cancer biology study design, using examples that illustrate specific challenges and solutions
Bad:
As it is well known, increased athletic activity has been related to a
profile of lower cardiovascular risk, lower blood pressure levels, and
improved muscular and cardio-respiratory performance.
Better:
Increased athletic activity is associated with lower cardiovascular risk, lower blood pressure, and improved fitness.
- or -
Increased athletic activity lowers cardiovascular risk and blood pressure, and improves fitness. (stronger level of evidence)
Bad:
The experimental demonstration is the first of its kind and is a proof of principle for the concept of laser driven particle acceleration in a structure loaded vacuum
Better:
The experiment provides the first proof of principle of laser-driven particle acceleration in a structure-loaded vacuum.
Bad:
Brain injury incidence shows two peak periods in almost all reports: rates are the highest in young people and the elderly.
Better:
Brain injury incidence peaks in the young and the elderly.
Bad:
A robust cell-mediated immune response is necessary, and deficiency in
this response predisposes an individual towards active TB
Better:
Deficiency in T-cell-mediated immune response predisposes an individual to active TB
Bad:
Anti-inflammatory drugs may be protective for the occurrence of Alzheimer’s Disease.
Better:
Anti-inflammatory drugs may protect against Alzheimer’s Disease.
Bad:
Clinical seizures have been estimated to occur in 0.5% to 2.3% of the neonatal population.
Better:
Clinical seizures occur in 0.5% to 2.3% of newborns.
Bad:
Ultimately p53 guards not only against malignant transformation but also plays a role in developmental processes as diverse as aging, differentiation, and fertility.
Better:
Besides preventing cancer, p53 also plays roles in aging, differentiation, and fertility.
Bad:
Injuries to the brain and spinal cord have long been known to be among the most devastating and expensive of all injuries to treat medically
Better:
Injuries to the brain and spinal cord are among the most devastating and
expensive.
Bad:
An IQ test measures an individual’s abilities to perform functions that usually fall in the domains of verbal communication, reasoning,
and performance on tasks that represent motor and spatial capabilities.
Better:
An IQ test measures an individual’s verbal, reasoning, or motor and spatial abilities.
Bad:
As we can see from Figure 2, if the return kinetic energy is less than 3.2 Up, there will be two electron trajectories associated with this kinetic energy.
Better:
Figure 2 shows that a return kinetic energy less than 3.2 Up yields two
electron trajectories.
Active voice:
She throws a ball.
- She: agent
- throws: verb
- the ball: recipient
Passive voice:
The ball is thrown by her.
- The ball: recipient
- is thrown: verb
- her: agent
Using active voice is more direct.
Reasons to use active voice:
-
Active voice emphasizes author responsibility.
No attempt was made to contact non-responders because they were deemed unimportant to the analysis.
should be
We did not attempt to contact non-responders because we deemed them unimportant to the analysis.
-
Active voice improves readability.
A strong correlation was found between use of the passive voice and other sins of writing.
should be
We found a strong correlation between use of passive voice and other sins of writing.
-
Active voice reduces ambiguity.
General dysfunction of the immune system at the leukocyte level is suggested by both animal and human studies.
should be
Both human and animal studies suggest that diabetics have general immune dysfunction at the leukocyte level.
Passive voice should be used sparingly and purposefully.
- e.g. In the methods section where what was done is more important than who did it.
Reasons:
- The active voice is livelier and easier to read.
- Avoiding personal pronouns does not make your science more objective.
- By agreeing to be an author on the paper, you are taking responsibility for its content. Thus, you should also claim responsibility for the assertions in the text by using “We” or “I”.
Additional Reasons:
- Journals want this! (e.g. Science magazine advises: “Use active voice when suitable, particularly when necessary for correct syntax" )
- Great authors do it! (Watson and Crick’s celebrated 1953 paper in Nature begins: “We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.).”)
All "to be" verbs and weak verbs should be replaced by more informative words.
"To be" verbs:
is, are, was, were, be, been, am, ...
Weak verbs:
come, move, report, provide, ...
- Examples
Loud music came from speakers embedded in the walls, and the entire arena moved as the hungry crowd got to its feet.
should be
Loud music exploded from speakers embedded in the walls, and the entire arena shook as the hungry crowd leaped to its feet.
and
The WHO reports that approximately two-thirds of the world’s diabetics are found in developing countries, and estimates that the number of diabetics in these countries will double in the next 25 years.
should be
The WHO estimates that two-thirds of the world’s diabetics are found in developing countries, and projects that the number of diabetics in these countries will double in the next 25 years.
Don’t kill verbs by turning them into nouns.
| Wrong | Right |
|---|---|
| Obtain estimates of | estimates |
| Has seen an expansion in | has expanded |
| Provides a methodological emphasis | emphasizes methodology |
| Take an assessment of | assess |
| provide a review of | review |
| offer confirmation of | confirm |
| make a decision | decide |
| shows a peak | peak |
| provide a description of | describe |
- Examples
During DNA damage, recognition of H3K4me3 by ING2 results in recruitment of Sin3/HDAC and repression of cell proliferation genes.
should be
During DNA damage, H3K4me3 recruits ING2 and Sin3/HDAC, which together repress cell proliferation genes.
Keep the subject and main verb (predicate) close together at the start of the sentence.
Readers are waiting for the verb!
- Examples
One study ... (long sentence) found that ...
should be
One study found that, ...
The word "data" is plural.
These data show an unusual trend.
The data support the conclusion.
The data are critical
- Affect is the verb “to influence”
- The class affected her.
- As a noun, affect denotes feeling or emotion shown by facial expression or body language.
- Effect is the noun form of this influence
- The class had an effect on her.
- As a verb, effect means to bring about or to cause, as in “to effect a change”
- Compare to = to point out similarities between different things
- Compare with (used more often in science) = to point out differences between similar things
Shall I compare thee to a summer’s day?
Brain tumors are relatively rare compared with more common cancers, such as those of the lung, breast, and prostate.
- “That” is the restrictive (defining) pronoun
- “Which” is the nonrestrictive (non-defining) pronoun
Key question: Is your clause essential or nonessential?
- THAT: The essential clause cannot be eliminated without changing the meaning of the sentence.
- WHICH: The non-essential clause can be eliminated without altering the basic meaning of the sentence (and must be set off by commas).
The bike *that* is broken is in the garage.
(Identifies which bike of many.)
The bike, *which* is broken, is in the garage.
(Adds a fact about the only bike in question).Do not use “they” or “their” when the subject is singular. To avoid gender choice, turn to a plural!
Each student worries about ~~their~~ grade.
Each student worries about her grade.
*Better*: All students worry about their grades.Bad:
The fear expressed by some teachers that students would not learn statistics well if they were permitted to use canned computer programs has not been realized in our experience. A careful monitoring of achievement levels before and after the introduction of computers in the teaching of our course revealed no appreciable change in students’ performances.
Better:
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 detriments in performance.
Bad:
Review of each center’s progress in recruitment is important to ensure that the cost involved in maintaining each center’s participation is worthwhile.
Better:
We should review each center’s recruitment progress to make sure its continued participation is cost-effective.
Bad:
It should be emphasized that these proportions generally are not the result of significant increases in moderate and severe injuries, but in many instances reflect mildly injured persons not being seen at a hospital.
Better:
Shifting proportions in injury severity may reflect stricter hospital admission criteria rather than true increases in moderate and severe injuries.
Bad:
Important studies to examine the descriptive epidemiology of autism, including the prevalence and changes in the characteristics
of the population over time, have begun.
Better:
Studies have begun to describe the epidemiology of autism, including recent changes in the disorder’s prevalence and characteristics.
Bad:
There are multiple other mechanisms that are important, but most of them are suspected to only have a small impact or are only important because of impact on one of the three primary mechanisms.
Better:
Multiple other mechanisms play only a small role or work by impacting one of the three primary mechanisms.
Bad:
After rejecting paths with poor signal-tonoise ratios, we were left with 678 velocity measurements of waves with 7.5 seconds period and 891 measurements of 15 second waves.
Better:
Rejecting paths with poor signal-to-noise ratios left 678 velocity measurements of 7.5-second waves and 891 of 15-second waves.
Bad:
It is suspected that the importance of temperature has more to do with impacting rates of other reactions than being a mechanism of disinfection itself since ponds are rarely hot enough for temperature alone to cause disinfection.
Better:
Ponds are rarely hot enough for temperature alone to cause disinfection; thus, the effect of temperature is likely mediated through its impact
on the rates of other reactions.
Bad:
It was assumed that due to reduced work at the joints of the lower limbs and less energy loss in the prosthetic leg, running with the dedicated
prostheses allows for maximum sprinting at lower metabolic costs than in the healthy ankle joint complex.
Better:
The prosthetic leg reduces work and energy loss compared with a healthy ankle joint, which may lead to lower metabolic costs during maximum sprinting.
Increasing power to separate (from low to high):
- Comma
, - Colon
: - Dash
- - Parentheses
() - Semicolon
; - Period
.
Notes:
,must follow an incomplete sentence.:,-can follow either complete or incomplete sentences.(),;,.should follow complete sentences.
Increasing formality (from low to high):
- Dash
- - Parentheses
() - The others (Comma
,, Colon:, Semicolon;, Period.)
- The semicolon
;connects two independent clauses.
(Note that a clause always contains a subject and predicate, and an independent clause can stand alone as a complete sentence.)
Kennedy could be a cold and vain man, and he led a life of privilege. But he knew something about the world; he also cared about it.
It was the best of times; it was the worst of times.
- The semicolon
;separates items in lists that contain internal punctuation (e.g.,).
It happened because people organized and voted for better prospects; because leaders enacted smart, forward-looking policies; because people's perspectives opened up, and with them, societies did too.
Here , can no longer separate the sentences because of internal ,, so use ;
- The parentheses
()inserts an afterthought or explanation (a word, phrase, or sentence) into a passage that is grammatically complete without it.- Info in
()should be additional material. ()de-emphasizes the inner information.- If you remove the material within the parentheses, the main point of the sentence should not change.
- Parentheses give the reader permission to skip over the material.
- But it can be a nice detail for readers.
- Info in
They also have a specialized tail, kind of like a monkey's tail, that allows them to cling to a piece of grass (or a lucky diver's finger).
This is troubling because, while there are plausible biological stories to connect red meat with cancer and heart disease, it seems unlikely that eating too much red meat could directly cause accidents and injuries. (Unless, as one of my student quipped, red meat eaters are swerving to avoid cows!)
- Use a colon after an independent clause to introduce a
- list
- quote
- explanation
- conclusion
- amplification
The hydrogen bonds are made as follows: purine position 1 to pyrimidine position 1; purine position 6 to pyrimidine position 6.
(Here, by using a colon, we're building up the reader's anticipation, we're getting them ready for the punchline.)
That's one reason why I'm so optimistic about the future: the constant churn of scientific progress.
The woman suffers from lack of experience and a chronic Democratic disease: compound sentences.
Companies use Marsh for the same reason that home sellers use real-estate agents: The agent's knowledge and experience is supposed to help the client get the right deal at the right place.
When it's arbitrary, 3 is a pleasing number of how many examples you list.
Two aspects of alcohol use are related to brain injuries: as a factor associated with risk of an injury such as a motor vehicle crash, and as a factor in TBI diagnosis, recovery, or survival after injury.
Issue:
- The aspects should be nouns, but it starts with
as.
Refined version:
Two aspects of alcohol use are related to brain injuries: its association with risk of injury, such as motor vehicle crash, and its post-injury influences on TBI diagnosis, recovery, or survival after injury.
In one project we have a nutritionist, a psychologist, statisticians, a computer specialist, and dietitians: a whole range of specialties.
Issues:
- Lists and the recipient
a whole range of specialtiesare inverse.
Refined version:
In one project we have a whole range of specialties: a nutritionist, a psychologist, statisticians, a computer specialist, and dietitians.
Use the dash to add emphasis or to insert an abrupt definition or description almost anywhere in the sentence
Just don't overuse it, or it loses its impact.
The drugs did more than prevent new fat accumulation. The also triggered overweight mice to shed significant amounts of fat - up to half their body weight.
- If using
,, loss of emphasis, more clunky - If using
(), it buries the information
Researchers who study shipworms say these mislabeled animals - they're clams, not worms - are actually a scientific treasure.
- commas aren't strong enough to set off a clause.
- If using
(), it buries the information
Writing sentences in parallel structures.
Pairs of ideas joined by and, or, or but should be written in parallel form.
- SVX but SVX
The velocity decreased by 50% but the pressure decreased by only 10%.
- Infinitive phrase and infinitive phrase
We aimed to increase the resolution and to improve picture quality.
- List of ideas
Locusts denuded fields in Utah, torrents washed away rural Iowa, and blazing heat shriveled Arizona's cotton.
Parallelism forces you to make a choice of the structure and stick to it.
- 1 paragraph = 1 idea
- Give away the punch line (conclusion) early
- "Inverse pyramid style" in Journalism
- Paragraph flow is helped by
- Logical flow of ideas
- parallel sentences and structures
- if necessary, transition words
- Make the last sentence memorable
- Emphasis at the end.
- Your reader remembers the first sentence and the last sentence best.
- Sequential in time
- Avoid the Memento approach!
- General -> specific
- Take-home message first!
- Logical arguments (if a then b; a; therefore b)
- Outline (What is the paragraph trying to convey?)
- Main idea of the paragraph
- Major points / supporting ideas
- Sub-supporting ideas
- The target is to bring out all relevant info and get rid of irrelevant info
- Re-organize sentences
- Boil sentences down to upshots
- Put upshots all together
- Re-order upshots and hence sentences
- Find and delete irrelevant info
- Sentence-level editing
The concept of chocolate having potential therapeutic benefits for people with diabetes mellitus, especially type 2 diabetes mellitus, presents a number of intellectual challenges, from both clinical and sociological perspectives. It seems almost counterintuitive to suggest an energy-dense food that is high in sugar, and often seen as a treat or a “dietary sin”, could offer such promise. However, a large volume of mechanistic and animal model studies has been undertaken demonstrating the potential benefits of cocoa and chocolate for both glucose regulation and modification of complications associated with diabetes. Cesar Fraga in the American Journal of Clinical Nutrition first proposed the potential of chocolate for people with diabetes in 2005. It was suggested that we should consume more cocoa and chocolate to reduce the burdens of hypertension and diabetes.(1) Grassi and colleagues (2) further reinforced this potential for its antihypertensive and insulin-sensitizing effect with the mechanistic data. However, the hypothesis of chocolate having a beneficial effect remains counterintuitive to the average consumer and has yet to gain support among the wider medical and healthcare community.
- Find the upshot for every sentence.
| Original | Upshot |
|---|---|
| The concept of chocolate having potential therapeutic benefits for people with diabetes mellitus, especially type 2 diabetes mellitus, presents a number of intellectual challenges, from both clinical and sociological perspectives. | It's surprising that chocolate might be healthy. |
| it seems almost counterintuitive to suggest an energy-dense food that is high in sugar, and often seen as a treat or a “dietary sin”, could offer such promise. | It's counterintuitive that chocolate might be healthy. |
| However, a large volume of mechanistic and animal model studies has been undertaken demonstrating the potential benefits of cocoa and chocolate for both glucose regulation and modification of complications associated with diabetes. | Many studies suggest chocolate is healthy. |
| Cesar Fraga in the American Journal of Clinical Nutrition first proposed the potential of chocolate for people with diabetes in 2005. | The first of these studies was in 2005. |
| It was suggested that we should consume more cocoa and chocolate to reduce the burdens of hypertension and diabetes.(1) | The study showed benefits for hypertension and diabetes. |
| Grassi and colleagues (2) further reinforced this potential for its antihypertensive and insulin-sensitizing effect with the mechanistic data. | Another study showed benefits for hypertension and diabetes. |
| However, the hypothesis of chocolate having a beneficial effect remains counterintuitive to the average consumer and has yet to gain support among the wider medical and healthcare community. | It's counterintuitive that chocolate might be healthy, so medical professionals are skeptical. |
- Re-org
| Original | Action |
|---|---|
| Many studies suggest chocolate is healthy. | Remain |
| The first of these studies was in 2005. | Remain |
| The study showed benefits for hypertension and diabetes. | These studies show ... |
| Another study showed benefits for hypertension and diabetes. | Delete |
| It's counterintuitive that chocolate might be healthy, so medical professionals are skeptical. | Medical professionals are skeptical |
| It's surprising that chocolate might be healthy. | Delete |
| It's counterintuitive that chocolate might be healthy. | Remain |
Edited version:
Many mechanistic and animal studies suggest health benefits for cocoa and chocolate particularly for patients with hypertension and type 2 diabetes. These studies suggest that cocoa and chocolate can lower blood pressure, improve glucose regulation, improve insulin sensitivity and reduce complications from diabetes. But the idea of chocolate is medicine has yet to gain widespread support among consumers or among the wider medical and health care community. It seems counterintuitive that a high sugar energy dense food - one often seen as a treat or dietary sin - could promote health.
It's okay to repeat a word. Sometimes, you do need repeating a word.
- You need to repeat keywords to keep consistent.
- e.g. name of comparison groups, variables, or instruments
Whereas it's just amusing or inelegant in some types of writing, in scientific writing it's a disaster.
The reader may think you are referring to a different instrument, model, group, variable, etc.
- Acronyms create new words; initialisms just use all first letters.
- Resist the temptation to abbreviate words simply because they occur frequently!
- Use only standard acronyms/initialisms. DON'T make them up!
- e.g. miR instead of micro RNA
- If you must use acronyms, define them separately in the abstract, each table/figure, and the text.
- For long papers, redefine occasionally (as readers don't typically read start to finish).
- Prewriting (70%)
- Collect, synthesise, and organise info
- Brainstorm take-home messages
- Work out ideas away from the computer
- Develop a roadmap/outline
- Writing the first draft (10%)
- Put facts/ideas together in organised prose
- Revision (20%)
- Read the work out loud
- Get rid of clutter
- Do a verb check
- Get feedback from others
Bad examples:
- What will happen if mixing prewriting and writing
- Write a paragraph, google for data/statistics/..., be distracted from the big picture, and the section ends up with chaos.
- What will happen if mixing writing and revision
- Be distracted by details and lose big pictures
- Get organised first!
- DON'T try to write and gather info simultaneously
- Gather and organise info BEFORE writing the first draft
- Have your own organisational system
- Read a lot of papers
- Write critical info in a single document
- Organise them
- Have the roadmap of the paper
- Develop the roadmap to a more detailed structure
- Stay away from the computer
- "Write" on the go!
- When exercising, driving, waiting, multitasking...
- Work out take-home messages
- Organise your paper
- Write memorable lines/words
- Similar paragraphs should be grouped/merged
- DON'T "Bait-and-Switch" readers too many times
- Bait-and-Switch: Argument for A, argument for B, argument for A, ...
- When discussing a controversy, follow this routine
- All arguments
- All counter-arguments
- All rebuttals
- DON'T be a perfectionist
- The goal of the first draft is to get the ideas down in complete sentences in order
- Focus on logical organisation more than sentence-level details
- Brain processes spoken words different than written words.
- Lackluster verbs (e.g., is, are)
- Passive verbs (e.g., was observed)
- Buried verbs (e.g., long_subject... verb... )
- Dead weight words/phrases (e.g., it should be emphasised that...)
- Empty words/phrases (e.g., basic tenets of, important)
- Long words/phrases that can be short
- Unnecessary jargon/acronyms
- Repetitive words/phrases (e.g., teaches clinicians/guides clinicians)
- Adverbs (e.g., very, really, quite, basically)
- Tag each paragraph with a phrase/sentence summarising the main point
- Move paragraphs abound to improve logical flow and bring similar ideas together
- Preferably outside your department
- Without technical background, they should easily grasp
- main findings
- take-home messages
- significance of the work
- Ask them to point out particularly hard-to-read sentences/paragraphs
- Find a good editor to edit your work
- Inconsistency
- Things that are contradictory in different places
- Do the numbers in the Abstract match the numbers in tables/figures/text?
- DO the numbers in the text match those in the tables/figures?
- Do the numbers in each table/figure match those in other tables/figure?
-
Do you have "reference to nowhere"?
-
Reference does not provide the indicated info/fact, including
- Authors misinterpreted/exaggerated the findings from the original source
- Reference cites a secondary source than a primary source (i.e., citation propagation).
- AUthors mis-numbered the references.
-
Always cite/go back to primary sources!
-
Assume that other authors have made errors in citing sources!
Bad:
In assessing the quality of an instrument we distinguish three quality domains, i.e. reliability, validity, and responsiveness. Each domain contains one or more measurement properties. The domain reliability contains three measurement properties: internal consistency, reliability, and measurement error. The domain validity also contains three measurement properties: content validity, construct validity, and criterion validity. The domain responsiveness contains only one measurement property, which is also called responsiveness. The term and definition of the domain and measurement property responsiveness are actually the same, but they are distinguished in the taxonomy for reasons of clarity. Some measurement properties contain one or more aspects, that were defined separately: Content validity includes face validity, and construct validity include structural validity, hypotheses testing, and cross-cultural validity.
Better:
We assess each instrument based on reliability, validity, and
responsiveness. These domains may be subdivided into measurement properties: Reliability includes internal consistency, reliability, and measurement error; validity includes content validity, construct validity, and criterion validity; responsiveness is both a domain and a measurement property. Some measurement properties additionally contain
multiple aspects; for example, construct validity includes structural validity, hypothesis testing, and cross-cultural validity.
Bad:
The church’s record-keeping system and its high level of accuracy has been previously reported (2). Briefly, the church creates and maintains a church record for each individual who is baptized into the church. These records are created at the congregation level at the time of baptism and then forwarded to the general church level where the membership record is added to the church membership database. These records contain minimal information including name, date of birth,
parents’ names, dates of church ordinances, and current address. Each congregation has a lay membership clerk who is responsible for updating the membership records for the members of the congregation. Such updates would include dates of ordinances received after baptism (e.g., priesthood ordination or marriage), name of spouse when a member marries, change of current address and date of death.
Better:
While the accuracy of the church record is dependent upon lay clerks within each congregation, each member has an opportunity to review their membership record once a year to check it for accuracy. For this reason and because the church emphasizes accurate record keeping, the information available from the church records is quite reliable, especially for members who are actively involved in the church. When
a member dies and the clerk reports his/her death to the Church Membership Council, the membership record is updated and then archived in the church’s deceased membership file.
Bad:
Previous studies have consistently reported increased risk of subsequent drug use associated with conduct problems and antisocial behavior in childhood (1-5), and an association of drug dependence with conduct problems was found in a general survey of young adults (9). Furthermore, long-term relationships between aggressive, unconventional, and impulsive behaviors have also been found with drug use involvement generally (10-12). However, different pathways between early childhood misbehavior and drug involvement may exist. Psychiatric symptoms and cognitive disabilities may be manifest as aggressive behaviors and drug use may be a response to impulsive tendencies that often co-occur with aggression or misbehavior. Distress and failure to adopt responsible conventional roles and behaviors may be important mediators linking childhood misbehavior to late drug dependence (13,14).
Better:
Previous studies have linked early childhood conduct problems with subsequent drug use (1-5). Studies have also found that young adult (9) and adult (10-12) drug users exhibit more aggressive, unconventional, and impulsive behaviors than their peers.
Several pathways may explain our finding: aggressive children may have underlying psychiatric disorders or cognitive disabilities that increase their risk of drug use; misbehavior tends to co-occur with impulsivity, which increases the risk of drug use; and childhood misbehavior may lead to long-term problems, such as persistent distress or a failure to ever adopt conventional roles or behaviors, which may lead to drug dependence (13,14).
- Break your writing task into small and realistic goals.
- Examples:
- My goal is to write 400 words today.
- My goal is to write the first two paragraphs of the discussion section today.
- Examples:
- Tables and Figures
- Results
- Methods
- Introduction
- Discussion
- Abstract
- Editors, reviewers, and readers may look first (and maybe only) at titles, abstracts, and tables and figures!
- Figures and tables should stand alone and tell a complete story. The reader should not need to refer back to the main text.
-
Use the fewest figures and tables needed to tell the story.
-
Do not present the same data in both a figure and a table.
- Figures
- Visual impact
- Show trends and patterns
- Tell a quick story
- Tell the whole story
- Highlight a particular result
- Tables
- Give precise values
- Display many values/variables
- Identify the specific topic or point of the table.
- Use the same key terms in the table title, the column headings, and the text of the paper
- Keep it brief!
- Example: “Descriptive characteristics of the two treatment groups, means ± SD or N (%)”
- Use superscript symbols to identify footnotes, according to journal guidelines;
- A standard series is: *, †,‡,¶,#,**,††, etc.
- Use footnotes to explain statistically significant differences
- E.g., *p<.01 vs. control by ANOVA
- Use footnotes to explain experimental details or abbreviations
- E.g., EDI is the Eating Disorder Inventory (reference)
- Amenorrhea was defined as 0-3 periods per year
Model your tables from already published tables! Don’t re-invent the wheel!!
-
Follow journal guidelines RE:
- Roman or Arabic numbers
- centered or flush left table number, title, column, headings, and data
- capital letters and italics
- the placement of footnotes
- the type of footnote symbols
-
Most journals use three horizontal lines: one above the column headings, one below the column headings, and one below the data
-
Don't use grid lines!
-
Make sure everything lines up and looks professional!
-
Use a reasonable number of significant figures.
-
Give units!
-
Omit unnecessary columns!
- Primary evidence
- electron micrographs, gels, photographs, pathology slides, X-rays, etc.
- indicates data quality
- “Seeing is believing”
- Graphs
- line graphs, bar graphs, scatter plots, histograms, boxplots, etc.
- Drawings and diagrams
- illustrate an experimental set-up or work-flow
- indicate flow of participants
- illustrate cause and effect relationships or cycles
- give a hypothetical model
- represent microscopic particles or microorganisms as cartoons
**Allows the figure to stand alone.
May contain:
- Brief title
- Essential experimental details
- Definitions of symbols or line/bar patterns
- Explanation of panels (A,B,C,D, etc.)
- Statistical information (tests used, p-values)
- Line graphs
- Used to show trends over time, age, or dose (can display group means or individuals)
- Bar Graphs
- Used to compare groups at one time point
- Tells a quick visual story
- Scatter Plots
- Used to show relationships between two variables (particularly linear correlation)
- Allows reader to see individual data points=more information!
- Tell a quick visual story
- Keep it simple!
- Make it easy to distinguish groups (e.g., triangles vs. circles vs. squares is not easy!)
- If it’s too complex, maybe it belongs in a table
- illustrate an experimental set-up or work-flow
- indicate flow of participants
- illustrate cause and effect relationships or cycles
- give a hypothetical model
- represent microscopic particles or microorganisms as cartoons
The results section should:
- Summarize what the data show
- Point out simple relationships
- Describe big-picture trends
- Cite figures or tables that present supporting data
- Avoid simply repeating the numbers that are already available in tables and figures.
Original:
The characteristics of the bad witches and the good witches are shown in Table 1. There was a significant difference in age between the groups. The mean age of the bad witches was 45 ± 5; and the mean age of the good witches was 36 ± 6. There was no significant difference in gender between the groups, with the bad witches having 85% females and the good witches having 83% females. BMI was not significantly different between the groups, which both had normal BMIs. Systolic blood pressure and exercise were significantly different. The bad witches had a mean blood pressure of 140 ± 10, whereas the good witches had a mean blood pressure of 120 ± 9. Estimated daily exercise was higher in the good witches (60 ± 30) than the bad witches (30 ± 20). Employment was not significantly different between the two groups…
Revised:
The witches were, on average, lean and predominantly female (Table 1). Bad witches were significantly older, had higher blood pressures, exercised less, and were more likely to smoke than good witches. More bad witches were unemployed, but this difference did not reach statistical significance.
- Break into subsections, with headings (if needed)
- Complement the information that is already in tables and figures
- Give precise values that are not available in the figure
- Report the percent change or percent difference if absolute values are given in the table
- Repeat/highlight only the most important numbers
- Don’t forget to talk about negative and control results
- Reserve the term “significant” for statistically significant
- Reserve information about what you did for the methods section
- In particular, do not discuss the rationale for statistical analyses within the Results section.
- Reserve comments on the meaning of your results for the discussion section
Use past tense for completed actions:
- We found that…
- The average reaction time was…
- Women were more likely to…
- Men smoked more cigarettes than…
Use the present tense for assertions that continue to be true, such as what the tables show, what you believe, and what the data suggest:
- Figure 1 shows…
- The findings confirm…
- The data suggest…
- We believe that this shows…
Since you can talk about the subjects of your experiments, “we” can be used sparingly while maintaining the active voice!
- Give a clear overview of what was done
- Give enough information to replicate the study (like a recipe!)
- Be complete, but make life easy for your reader!
- Break into smaller sections with subheadings
- Cite a reference for commonly used methods
- Display in a flow diagram or table where possible
-
You may use jargon and the passive voice more liberally in the methods section
-
Answers the Who, what, when, where, how, and why…
-
Yes. You can use figures in your method section if it makes the explanation easier
- Materials
- Drugs, buffers, chemicals, gases, reagents, cell lines, etc.
- Participants/subjects
- Animals (state that the research was approved by the appropriate committee at your institution)
- Humans (state that the research was approved by the appropriate committee at your institution)
- Experimental protocol/study design
- Measurements
- How were the dependent and independent variables measured
- Instruments (telescope, microscope, weighing scale, questionnaire, etc.)
- How were the dependent and independent variables measured
- Analyses
- Report methods in past tense (“we measured”),
- But use present tense to describe how data are presented in the paper (“data are summarized as means +- SD”)
Passive:
- E.g., Oral temperatures were measured.
- Emphasizes the method or variable.
Active:
- E.g., We measured oral temperatures
- More lively, but sacrifices having the material/method/variable as the subject of the sentence
- Requires creativity to avoid starting every sentence with We!
Even jargon is OK!
- Good News: The introduction is easier to write than you may realize!
- Follows a fairly standard format
- Typically 3 paragraphs long
- Recommended range: 2 to 5
- It is not an exhaustive review of your general topic
- should focus on the specific hypothesis/aim of your study
Narrow down from general to specific:
- Background, known information
- Knowledge gap, unknown information
- Hypothesis, question, purpose statement
- Approach, plan of attack, proposed solution
1. First
- What’s known
2. Second
- What’s unknown
- limitations and gaps in previous studies
3. Third
- Your burning question
- Your experimental approach
- Why your experimental approach is new and different and important (fills in the gaps)
- Keep paragraphs short
- Write for a general audience
- clear, concise, non-technical
- Take the reader step by step from what is known to what is unknown. End with your specific question.
- Known -> Unknown -> Question/hypothesis
- Emphasize how your study fills in the gaps (the unknown)
- Explicitly state your research question/aim/hypothesis:
- “We asked whether”; “Our hypothesis was”; “We tested the hypothesis that”; “Our aim/s were”
- Do not answer the research question (no results or implications).
- Summarize at a high level! Leave detailed descriptions, speculations, and criticisms of particular studies for the discussion.
The Discussion section…
- Gives you the most freedom
- Gives you the most chance to put good writing on display
- Is the most challenging to write
- Answer the question asked.
- Support your conclusion (your data, other's data)
- Defend your conclusion (anticipate criticisms)
- Give the "big-picture" take-home message
i.e. what do my results mean and why should anyone care?
- Key finding (answer to the question(s) asked in Intro.)
- Start with: “WE FOUND THAT…” (or something similar)
- Explain what the data mean (big-picture!)
- State if the findings are novel
- Key secondary findings
- Context
- Give possible mechanisms or pathways
- Compare your results with other people’s results
- Discuss how your findings support or challenge the paradigm
- Strengths and limitations
- Anticipate readers’ questions/criticisms
- Explain why your results are robust
- What's next
- Recommended confirmatory studies (“needs to be confirmed”)
- Point out unanswered questions and future directions
- The “so what?”: implicate, speculate, recommend
- Give the big-picture (human) implications of basic science findings
- Tell readers why they should care
- Strong conclusion
- Restate your main finding.
- Give a final take-home message.
- Showcase good writing!
- Use the active voice
- Tell it like a story
- Start and end with the main finding
- “We found that…”
- Don’t travel too far from your data
- Focus on what your data do prove, not what you had hoped your data would prove
- Focus on the limitations that matter, not generic limitations
- Make sure your take-home message is clear and consistent
Past, when referring to study details, results, analyses, and background research:
- We found that
- Subjects may have experienced
- Miller et al. found
Present, when talking about what the data suggest:
- The greater weight loss suggests
- The explanation for this difference is not clear.
- Potential explanations include
Abstracts (ab=out, trahere=pull; “to pull out”)
- Overview of the main story
- Gives highlights from each section of the paper
- Limited length (100-300 words, typically)
- Stands on its own
- Most often, the only part people read!
- Background
- Question/aim/hypothesis
- “We asked whether,” “We hypothesized that,”…etc .
- Experiment(s)
- Quick summary of key materials and methods
- Results
- Key results found
- Minimal raw data (prefer summaries)
- Conclusion: The answer to the question asked/take home message
- Implication, speculation, or recommendation
Abstracts may be structured (with subheadings) or free-form.
Objectives To assess the amount, relevance, content, and suppressibility of academic electronic spam invitations to attend conferences or submit manuscripts. Design Prospective cohort study. Setting Email accounts of participating academics. Participants Five intrepid academics and a great many publishers, editors, and conference organizers. Intervention Unsubscribing from sender’s distribution lists. Main outcome measures Number of spam invitations received before, immediately after, and one year after unsubscribing from senders’ distribution lists. The proportion of duplicate invitations was also assessed and the relevance of each invitation graded to the recipient’s research interests. A qualitative assessment of the content of spam invitations was conducted.
- Results At baseline, recipients received an average of 312 spam invitations each month. Unsubscribing reduced the frequency of the invitations by 39% after one month but by only 19% after one year. Overall, 16% of spam invitations were duplicates and 83% had little or no relevance to the recipients’ research interests. Spam invitations were characterized by inventive language, flattery, and exuberance, and they were sometimes baffling and amusing.
- Conclusions Academic spam is common, repetitive, often irrelevant, and difficult to avoid or prevent.
Passing off other people’s writing (or tables and figures) as your own.
- Includes:
- cutting and pasting sentences or even phrases from another source
- slightly rewriting or re-arranging others’ words
- “borrowing” material from sites like Wikipedia
Original Version (Wikipedia):
Ernest Miller Hemingway (July 21, 1899– July 2, 1961) was an American author and journalist. His economical and understated style had a strong influence on 20th-century fiction, while his life of adventure and his public image influenced later generations. (Source: Wikipedia)
Plagiarized Version:
Ernest Hemingway’s thrifty and understated style strongly influenced 20th-century fiction. His audacious lifestyle and public image also influenced later generations.
Original passage (Klibanski et al. 1995):
“Our data demonstrate that, despite its usefulness in perimenopausal women, estrogen and progestin administration does not reverse the profound osteopeniaseen in all young women with anorexia nervosa. Trabecular bone loss is severe and may progress despite estrogen therapy.”
Plagiarized passage (Munoz et al. 2002):
“In conclusion, our data demonstrate that, despite its usefulness in perimenopausal women, estrogen and progestin administration does not reverse the profound osteopenia seen in all young women with AN. Trabecular bone loss is severe and may progress despite estrogen therapy.”
Original passage (Klibanski et al. 1995):
“There are no prospective studies of trabecular BD in adult women with anorexia nervosa, and it is unknown whether there is a progressive and permanent decline in bone mass. Although the role of estrogen replacement therapy in preventing bone loss in premenopausal women is clearly established, no studies have addressed whether is is beneficial in young women with premenopausal osteopenia.”
Plagiarized passage (Munoz et al. 2002):
“There are some published data on trabecular bone mineral density (BMD) in adult women with AN. but it is still unknown whether there is a progressive or permanent decline in bone mass. Although the role of estrogen replacement therapy in preventing bone loss in menopausal women has been clearly established, no studies have been carried out to determine whether it is beneficial in young women with premenopausal osteopenia”
- You must understand the material well enough to put it in your own words!
- Work from memory
- Draw your own conclusions
- Do not mimic the original author’s sentence structure or just re-arrange the original author’s words.
Recycling your own writing or data, including:
- Copying or only slightly rewriting text from your own previously published papers.
- Adding new data to already published data and presenting it as new results.
- Submitting identical or overlapping data to multiple journals.
- In pilot studies, publishers that used CrossCheck to look for plagiarism had to reject 6% to 23% of submitted papers (due to plagiarism or self plagiarism/duplication).
- 2-year study of plagiarism in the Croatian Medical Journal (automatic detection software followed by manual confirmation):
- 8% of papers plagiarized others’ work
- 3% of papers were self-plagiarized
- Strunk and White’s classic, The Elements of Style, http://www.bartleby.com/141/
- Clinical Chemistry Guide to Scientific Writing: http://www.aacc.org/publications/clin_chem/ccgsw/Pages/default.aspx#
- Mimi Zeiger. Essentials of Writing Biomedical Research Papers, McGraw Hill Professional