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Scientific Writing Workshop 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 reasonable 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.”

Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

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Page 1: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Scientific Writing Workshop

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 reasonable 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.

Page 2: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Dear Dr. Pallanck,Your piece was very long and wordy and I tried toslightly reduce some of the verbiage. I was carefulto edit judiciously. I found your piece extremely repetitive in places.Sincerely, a PNAS editor

Writing is difficult.

Dear Dr. Pallanck,Yours was one of the rare pieces that required little editing. I wish that more authors could write as clearly and with purpose. It was truly a pleasure to work with you.Sincerely, another PNAS editor

Writing can get better.

Page 3: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Workshop Outline:

I.What should be in a science abstract?II.How to write a sentence: Characters & ActionsIII.Passive vs. Active voiceIV.How to write a paragraph: Cohesion & CoherenceV.How to write concisely

Page 4: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

ABSTRACT

Provides a brief (often 250 words or less) summary of your work. Should include the following: Introduction; Question or Hypothesis addressed by the work; Materials and Methods (optional); Results; Discussion.

Probably the most important part of a manuscript or grant application.-Many people will read only the abstract.-The abstract of a grant application will direct the grant to the appropriate reviewers; will create the first impression of the quality of the application.

A Good Example:Loss-of-function mutations in PINK1 and Parkin cause parkinsonism in humans and mitochondrial dysfunction in model organisms. Parkin is selectively recruited from the cytosol to damaged mitochondria to trigger their autophagy. How Parkin recognizes damaged mitochondria, however, is unknown. Here, we show that expression of PINK1 on individual mitochondria is regulated by voltage-dependent proteolysis to maintain low levels of PINK1 on healthy, polarized mitochondria, while facilitating the rapid accumulation of PINK1 on mitochondria that sustain damage. PINK1 accumulation on mitochondria is both necessary and sufficient for Parkin recruitment to mitochondria, and disease-causing mutations in PINK1 and Parkin disrupt Parkin recruitment and Parkin-induced mitophagy at distinct steps. These findings provide a biochemical explanation for the genetic epistasis between PINK1 and Parkin in Drosophila melanogaster. In addition, they support a novel model for the negative selection of damaged mitochondria, in which PINK1 signals mitochondrial dysfunction to Parkin, and Parkin promotes their elimination.

Page 5: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

ABSTRACT

Provides a brief (often 250 words or less) summary of your work. Should include the following: Introduction; Question or Hypothesis addressed by the work; Materials and Methods (optional); Results; Discussion.

Probably the most important part of a manuscript or grant application.-Many people will read only the abstract.-The abstract of a grant application will direct the grant to the appropriate reviewers; will create the first impression of the quality of the application.

A Good Example:Loss-of-function mutations in PINK1 and Parkin cause parkinsonism in humans and mitochondrial dysfunction in model organisms. Parkin is selectively recruited from the cytosol to damaged mitochondria to trigger their autophagy. How Parkin recognizes damaged mitochondria, however, is unknown. Here, we show that expression of PINK1 on individual mitochondria is regulated by voltage-dependent proteolysis to maintain low levels of PINK1 on healthy, polarized mitochondria, while facilitating the rapid accumulation of PINK1 on mitochondria that sustain damage. PINK1 accumulation on mitochondria is both necessary and sufficient for Parkin recruitment to mitochondria, and disease-causing mutations in PINK1 and Parkin disrupt Parkin recruitment and Parkin-induced mitophagy at distinct steps. These findings provide a biochemical explanation for the genetic epistasis between PINK1 and Parkin in Drosophila melanogaster. In addition, they support a novel model for the negative selection of damaged mitochondria, in which PINK1 signals mitochondrial dysfunction to Parkin, and Parkin promotes their elimination.

Page 6: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

ABSTRACT

Provides a brief (often 250 words or less) summary of your work. Should include the following: Introduction; Question or Hypothesis addressed by the work; Materials and Methods (optional); Results; Discussion.

Probably the most important part of a manuscript or grant application.-Many people will read only the abstract.-The abstract of a grant application will direct the grant to the appropriate reviewers; will create the first impression of the quality of the application.

A Good Example:Loss-of-function mutations in PINK1 and Parkin cause parkinsonism in humans and mitochondrial dysfunction in model organisms. Parkin is selectively recruited from the cytosol to damaged mitochondria to trigger their autophagy. How Parkin recognizes damaged mitochondria, however, is unknown. Here, we show that expression of PINK1 on individual mitochondria is regulated by voltage-dependent proteolysis to maintain low levels of PINK1 on healthy, polarized mitochondria, while facilitating the rapid accumulation of PINK1 on mitochondria that sustain damage. PINK1 accumulation on mitochondria is both necessary and sufficient for Parkin recruitment to mitochondria, and disease-causing mutations in PINK1 and Parkin disrupt Parkin recruitment and Parkin-induced mitophagy at distinct steps. These findings provide a biochemical explanation for the genetic epistasis between PINK1 and Parkin in Drosophila melanogaster. In addition, they support a novel model for the negative selection of damaged mitochondria, in which PINK1 signals mitochondrial dysfunction to Parkin, and Parkin promotes their elimination.

Page 7: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

ABSTRACT

Provides a brief (often 250 words or less) summary of your work. Should include the following: Introduction; Question or Hypothesis addressed by the work; Materials and Methods (optional); Results; Discussion.

Probably the most important part of a manuscript or grant application.-Many people will read only the abstract.-The abstract of a grant application will direct the grant to the appropriate reviewers; will create the first impression of the quality of the application.

A Good Example:Loss-of-function mutations in PINK1 and Parkin cause parkinsonism in humans and mitochondrial dysfunction in model organisms. Parkin is selectively recruited from the cytosol to damaged mitochondria to trigger their autophagy. How Parkin recognizes damaged mitochondria, however, is unknown. Here, we show that expression of PINK1 on individual mitochondria is regulated by voltage-dependent proteolysis to maintain low levels of PINK1 on healthy, polarized mitochondria, while facilitating the rapid accumulation of PINK1 on mitochondria that sustain damage. PINK1 accumulation on mitochondria is both necessary and sufficient for Parkin recruitment to mitochondria, and disease-causing mutations in PINK1 and Parkin disrupt Parkin recruitment and Parkin-induced mitophagy at distinct steps. These findings provide a biochemical explanation for the genetic epistasis between PINK1 and Parkin in Drosophila melanogaster. In addition, they support a novel model for the negative selection of damaged mitochondria, in which PINK1 signals mitochondrial dysfunction to Parkin, and Parkin promotes their elimination.

Page 8: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

ABSTRACT

Provides a brief (often 250 words or less) summary of your work. Should include the following: Introduction; Question or Hypothesis addressed by the work; Materials and Methods (optional); Results; Discussion.

Probably the most important part of a manuscript or grant application.-Many people will read only the abstract.-The abstract of a grant application will direct the grant to the appropriate reviewers; will create the first impression of the quality of the application.

A Good Example:Loss-of-function mutations in PINK1 and Parkin cause parkinsonism in humans and mitochondrial dysfunction in model organisms. Parkin is selectively recruited from the cytosol to damaged mitochondria to trigger their autophagy. How Parkin recognizes damaged mitochondria, however, is unknown. Here, we show that expression of PINK1 on individual mitochondria is regulated by voltage-dependent proteolysis to maintain low levels of PINK1 on healthy, polarized mitochondria, while facilitating the rapid accumulation of PINK1 on mitochondria that sustain damage. PINK1 accumulation on mitochondria is both necessary and sufficient for Parkin recruitment to mitochondria, and disease-causing mutations in PINK1 and Parkin disrupt Parkin recruitment and Parkin-induced mitophagy at distinct steps. These findings provide a biochemical explanation for the genetic epistasis between PINK1 and Parkin in Drosophila melanogaster. In addition, they support a novel model for the negative selection of damaged mitochondria, in which PINK1 signals mitochondrial dysfunction to Parkin, and Parkin promotes their elimination.

Page 9: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Portion of the first sentence from an abstract in a recent issue of PNAS:Two approaches, one novel, are applied to analyze the divergent evolution of …

Portion of the last sentence from an abstract in a recent issue of Molecular Biology and Evolution:…our results have some implications regarding the means by which terpene synthases specify product outcome.

A few bad examples from the literature:

-One approach is new and interesting; the other is old and boring

“some implications” suggests that the implications were not important enough to mention in the abstract-not really a great way to end the abstract

Page 10: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Middle portion of an abstract in a recent issue of Cell:… Liver stages of the parasite containing thousands of merozoites grow inside hepatocytes for several days without triggering an inflammatory response. We show here that Plasmodium uses a PEXEL/VTS motif to introduce the circumsporozoite (CS) protein into the hepatocyte cytoplasm and a nuclear localization signal (NLS) to enter its nucleus. CS outcompetes NFκB nuclear import, thus downregulating the expression of many genes controlled by NFκB, including those involved in inflammation. CS also influences the expression of over one thousand host genes involved in diverse metabolic processes to create a favorable niche for the parasite growth…

Liver stages of the parasite containing thousands of merozoites grow inside hepatocytes…-Do the liver stages contain thousands of merozoites or does the liver?-Can the liver stages grow inside anything besides hepatocytes?

…Plasmodium uses a PEXEL/VTS motif…and a nuclear localization signal (NLS) to enter its nucleus-Does Plasmodium enter the nucleus or does the CS protein?

CS outcompetes NFκB nuclear import…-Does CS outcompete NFκB nuclear import or does CS nuclear import outcompete NFκB nuclear import?

…over one thousand host genes involved in diverse metabolic processes to create a favorable niche for the parasite growth-Are the one thousand genes creating a favorable niche, or are the diverse metabolic processes creating the niche?

Page 11: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Workshop Outline:

I.What should be in a science abstract?II.How to write a sentence: Characters & ActionsIII.Passive vs. Active voiceIV.How to write a paragraph: Cohesion & CoherenceV.How to write concisely

But first, some basic grammatical terms…

Page 12: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Definitions of Some Basic Grammatical Terms

A. PARTS OF SPEECHNOUN -- 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.

Page 13: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

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.

Page 14: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

B. SENTENCE ELEMENTSSUBJECT -- 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 ("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.

Page 15: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Characters and Actions

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.

Page 16: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Characters and Actions

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

Page 17: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Characters and Actions

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

Page 18: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Characters and Actions

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 charactersVERBS

In a clear sentence, the main characters are subjects and verbs name the actions of the characters.

Page 19: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

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?

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

In a clear sentence, the main characters are subjects and verbs name the actions of the characters.

argument

federalists, government, popular democracy, factions

was based, further

argue, destabilize, believe, further

Page 20: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

NominalizationsWriting 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.

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.

Adjective Nominalizationcareless carelessnessdifferent differenceproficient proficiencyknow knowledge

Examples:Verb NominalizationDiscover discoveryResist resistancereact reactionutilize, use Utilizationreduce reduction

Page 21: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

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.

Readers prefer your subjects be characters and your verbs be actions.

Page 22: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Workshop Outline:

I.What should be in a science abstract?II.How to write a sentence: Characters & ActionsIII.Passive vs. Active voiceIV.How to write a paragraph: Cohesion & CoherenceV.How to write concisely

Page 23: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Active vs. Passive voice

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.

ActiveJohn ate the apples.John, the subject, is the one performing the action of the verb.

PassiveThe apples were eaten by John.The apples, the subject in this sentence, are receiving the action of the verb.

Recognizing Passive ConstructionsStep 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.

Page 24: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

The passive voice in science writingThe 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]

Page 25: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

-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.

Page 26: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Workshop Outline:

I.What should be in a science abstract?II.How to write a sentence: Characters & ActionsIII.Passive vs. Active voiceIV.How to write a paragraph: Cohesion & CoherenceV.How to write concisely

Page 27: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Cohesion and Coherence

Cohesion: when pairs of sentences fit neatly together.

Principles of cohesion: 1. Begin sentences with information that is familiar (the ‘topic’ position). 2. End sentences with information readers cannot anticipate (the ‘stress’ position).

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.

The TOPIC positionIdeally, the topic of a sentence (what the sentence is about) will be its grammatical subject.

Not this: It is likely that our proposals will be accepted.

This: Our proposals will likely be accepted.

Page 28: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Cohesion and Coherence

Cohesion: when pairs of sentences fit neatly together.

Principles of cohesion: 1. Begin sentences with information that is familiar (the ‘topic’ position). 2. End sentences with information readers cannot anticipate (the ‘stress’ position).

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.

The TOPIC positionIdeally, the topic of a sentence (what the sentence is about) will be its grammatical subject.

Not this: It is likely that our proposals will be accepted.

This: Our proposals will likely be accepted.

Page 29: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Cohesion and Coherence

Cohesion: when pairs of sentences fit neatly together.

Principles of cohesion: 1. Begin sentences with information that is familiar (the ‘topic’ position). 2. End sentences with information readers cannot anticipate (the ‘stress’ position).

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.

The TOPIC positionIdeally, the topic of a sentence (what the sentence is about) will be its grammatical subject.

Not this: It is likely that our proposals will be accepted.

This: Our proposals will likely be accepted.

Page 30: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Cohesion and Coherence

Cohesion: when pairs of sentences fit neatly together.

Principles of cohesion: 1. Begin sentences with information that is familiar (the ‘topic’ position). 2. End sentences with information readers cannot anticipate (the ‘stress’ position).

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.

The TOPIC positionIdeally, the topic of a sentence (what the sentence is about) will be its grammatical subject.

Not this: It is likely that our proposals will be accepted.

This: Our proposals will likely be accepted.

Coherence: when all of the individual sentences in a passage support a larger point or claim.

Principle of coherence: The topics of each sentence in the passage should constitute a relatively small set of related ideas.

Page 31: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Are the sentences in the following passage cohesive? Is the passage coherent?

Saynor, Wisconsin, is the snowmobile capital of the world. The buzzing of snowmobile engines fills the air, and their tanklike tracks crisscross the snow. The snow reminds me of mom’s mashed potatoes, covered with furrows I would draw with my fork. Her mashed potatoes usually make me sick, that’s why I play with them. I like to make a hole in the middle of the potatoes and fill it with melted butter. This behavior has been the subject of long chats between me and my analyst.

Page 32: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Are the sentences in the following passage cohesive? Is the passage coherent?

Saynor, Wisconsin, is the snowmobile capital of the world. The buzzing of snowmobile engines fills the air, and their tanklike tracks crisscross the snow. The snow reminds me of mom’s mashed potatoes, covered with furrows I would draw with my fork. Her mashed potatoes usually make me sick, that’s why I play with them. I like to make a hole in the middle of the potatoes and fill it with melted butter. This behavior has been the subject of long chats between me and my analyst.

Grammatical subjects: Saynor, Wisconsin; buzzing of snowmobile engines; snow; mashed potatoes; I; This behavior

Page 33: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Are the sentences in the following passage cohesive? Is the passage coherent?

Saynor, Wisconsin, is the snowmobile capital of the world. The buzzing of snowmobile engines fills the air, and their tanklike tracks crisscross the snow. The snow reminds me of mom’s mashed potatoes, covered with furrows I would draw with my fork. Her mashed potatoes usually make me sick, that’s why I play with them. I like to make a hole in the middle of the potatoes and fill it with melted butter. This behavior has been the subject of long chats between me and my analyst.

Grammatical subjects: Saynor, Wisconsin; buzzing of snowmobile engines; snow; mashed potatoes; I; This behavior

Actions: is; fills the air & crisscross the snow; reminds, covered & draw; make me sick & play; like to make a hole & fill it; has been

Too many different subjects; too many different actions No coherent theme

Page 34: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Are the sentences in the following passage cohesive? Is the passage coherent?

Hypophysectomy (surgical removal of the pituitary) dramatically reduces circulating growth hormone (GH), insulin-like growth factor-1 (IGF-1), and thyroid hormones, and can extend life span in rats; these effects are similar to those of the Snell and Ames dwarf mutations in mice, which genetically ablate these pituitary hormones. Dwarf mice out-live normal controls and dwarfs exhibit many forestalled phenotypes of aging. But because these mutations confer lifelong hormonal deficits that slow growth, alter development and prevent reproduction, the relationship of these models to normal mammalian aging has been questioned. Furthermore, if the life span extension of dwarf mice is dependent on developmental abnormalities (especially at the expense of fecundity), clinical relevance of these models is limited. This interplay between development and aging is difficult to assess in mutant dwarf mice; however, age-specific effects can be defined in normal mice using hypophysectomy.

Page 35: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Are the sentences in the following passage cohesive? Is the passage coherent?

Hypophysectomy (surgical removal of the pituitary) dramatically reduces circulating growth hormone (GH), insulin-like growth factor-1 (IGF-1), and thyroid hormones, and can extend life span in rats; these effects are similar to those of the Snell and Ames dwarf mutations in mice, which genetically ablate these pituitary hormones. Dwarf mice out-live normal controls and dwarfs exhibit many forestalled phenotypes of aging. But because these mutations confer lifelong hormonal deficits that slow growth, alter development and prevent reproduction, the relationship of these models to normal mammalian aging has been questioned. Furthermore, if the life span extension of dwarf mice is dependent on developmental abnormalities (especially at the expense of fecundity), clinical relevance of these models is limited. This interplay between development and aging is difficult to assess in mutant dwarf mice; however, age-specific effects can be defined in normal mice using hypophysectomy.

Subjects/topics

Page 36: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Are the sentences in the following passage cohesive? Is the passage coherent?

Hypophysectomy (surgical removal of the pituitary) dramatically reduces circulating growth hormone (GH), insulin-like growth factor-1 (IGF-1), and thyroid hormones, and can extend life span in rats; these effects are similar to those of the Snell and Ames dwarf mutations in mice, which genetically ablate these pituitary hormones. Dwarf mice out-live normal controls and dwarfs exhibit many forestalled phenotypes of aging. But because these mutations confer lifelong hormonal deficits that slow growth, alter development and prevent reproduction, the relationship of these models to normal mammalian aging has been questioned. Furthermore, if the life span extension of dwarf mice is dependent on developmental abnormalities (especially at the expense of fecundity), clinical relevance of these models is limited. This interplay between development and aging is difficult to assess in mutant dwarf mice; however, age-specific effects can be defined in normal mice using hypophysectomy.

Subjects/topics

Rewriting to reduce the number of subjects yields: The surgical removal of the pituitary, known as hypophysectomy, dramatically reduces circulating growth hormone (GH), insulin-like growth factor-1 (IGF-1), and thyroid hormones, and can extend life span in rats; its effects are similar to those of the mouse Snell and Ames dwarf mutations, which genetically ablate these pituitary hormones. The Dwarf mutations result in mice that out-live normal controls and exhibit many forestalled phenotypes of aging. But these mutations confer lifelong hormonal deficits that slow growth, alter development and prevent reproduction, and thus the mutant mice may be a poor model for mammalian aging. Furthermore, if the dwarf mice live longer solely because of developmental abnormalities and reduced fecundity, their relevance to clinical studies is especially limited. Thus, dwarf mice are not useful to assess the interplay between development and aging, whereas normal mice that have undergone hypophysectomy permit age-specific effects to be defined.

Page 37: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

[Winslow Homer] arrived in Manhattan in 1859, at a time when war was breaking out, causing him to go to the front as an illustrator for Harper’s Weekly, the Life of its day. His manner, a plainspoken charm that put soldiers and their officers at ease, would make him a model for today’s embedded journalist. In that first year of the war, his production included a lot of standard wish-fulfillment military scenes, charges and flag-waving resistance, copied implicitly from old battle art. The early, showily Napoleonic phase of the war saw him spending time with the Zouave regiments of the Army of the Potomac, who wore red pantaloons, red fezzes, and blue collarless jackets. (Homer kept the fez, and wore it on occasion throughout his life.)

[Winslow Homer] arrived in Manhattan in 1859 and, when the war broke out, quickly went to the front as an illustrator for Harper’s Weekly, the Life of its day. He was, from the first, a plainspoken man who felt at home with soldiers and their officers — the model of an embedded journalist. In that first year of the war, he produced a lot of standard wish-fulfillment military scenes, charges and flag-waving resistance, copied implicitly from old battle art. In the early, showily Napoleonic phase of the war, he seems to have spent time with the Zouave regiments of the Army of the Potomac, who wore red pantaloons, red fezzes, and blue collarless jackets. (Homer kept the fez, and wore it on occasion throughout his life.)

Adam Gopkin, The New Yorker, October 31, 2005

Page 38: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Diagnosing your own writing:1. Do the first seven or eight words of every sentence (and clause) constitute a relatively small set of related ideas?2. Do those words name your most important characters?3. Are the topics of those sentences the grammatical subjects?

Is a sequence of identical topics in a passage monotonous?

Page 39: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Diagnosing your own writing:1. Do the first seven or eight words of every sentence (and clause) constitute a relatively small set of related ideas?2. Do those words name your most important characters?3. Are the topics of those sentences the grammatical subjects?

Is a sequence of identical topics in a passage monotonous?Probably not for the reader (in many instances). For the sake of clarity, it is often better to err on the side of consistency, than variety.

Page 40: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Diagnosing your own writing:1. Do the first seven or eight words of every sentence (and clause) constitute a relatively small set of related ideas?2. Do those words name your most important characters?3. Are the topics of those sentences the grammatical subjects?

Is a sequence of identical topics in a passage monotonous?Probably not for the reader (in many instances). For the sake of clarity, it is often better to err on the side of consistency, than variety.

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.

The next sentence in the above passage could begin with a new but familiar term:

Astronomers have recently reported, for example, that…

Page 41: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

The STRESS positionReaders want the Stress position (the last few words of a sentence or passage) to communicate:

i. Long and complex phrases:

Not this: A sociometric and actuarial analysis of Social Security revenues and disbursements for the last six decades to determine changes in projecting deficits is the subject of this study.

This: In this study, we analyze Social Security’s revenues and disbursements for the last six decades, using sociometric and actuarial criteria to determine changes in projecting deficits.

ii. New information, particularly unfamiliar technical terms:

Not this: lympokine-activated killer (LAK) cells are lymphoid cells that can lyse fresh, noncultured, natural-killer-cell-resistant tumor cells but not normal cells and are produced by incubating lymphocytes with the lympokine, interleukin-2.

This: The incubation of peripheral-blood lymphocytes with a lympokine, interleukin-2, generates lymphoid cells that can lyse fresh, noncultured, natural-killer-cell-resistant tumor cells but not normal cells. We term these cells lympokine-activated killer (LAK) cells.

Page 42: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior in the way we act in situations we are in every day.

Page 43: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior in the way we act in situations we are in every day.

Page 44: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior.

Page 45: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior.

B. Shift peripheral ideas to the left.The data offered to prove ESP are too weak for the most part.

Page 46: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior.

B. Shift peripheral ideas to the left.The data offered to prove ESP are too weak for the most part.

Page 47: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior.

B. Shift peripheral ideas to the left.The data offered to prove ESP are too weak for the most part. For the most part, the data offered to prove ESP are too weak.

Page 48: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior.

B. Shift peripheral ideas to the left.The data offered to prove ESP are too weak for the most part. For the most part, the data offered to prove ESP are too weak.

Sentences are cohesive with one another when we see at the beginning of a second sentence information that appeared toward the end of the preceding sentence.

Page 49: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

iii. Emphasis (the significant information in the sentence):

Some ways to manage endings for emphasis:A. Trim the end.Some sociobiologists claim that our genes control our social behavior.

B. Shift peripheral ideas to the left.The data offered to prove ESP are too weak for the most part. For the most part, the data offered to prove ESP are too weak.

Sentences are cohesive with one another when we see at the beginning of a second sentence information that appeared toward the end of the preceding sentence.

Passages are coherent when we see that the topics of each sentence in the passage constitute a relatively small set of related ideas.

Page 50: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Creating Coherence

• Can readers see the point of each section?Highlight the sentence that states the point of each section.Read those short opening segments as if they were a paragraph.

If they do not make sequential sense, revise them so that they do.

• Can readers see how everything is relevant to a point?Identify the relevance of each section or sentence to its point.

If you cannot identify the relevance of anything, clarify or cut it.

• Can readers see how subjects/topics in sentences in a section are a related string of familiar characters?

For each sentence in a section, underline its first several words.If those words are not subject/topics making a set of related words that name your main characters, revise so they are.

Do the underlined words name concepts that readers would expect, given the topic or previous sentence?

If not, revise.

Page 51: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Workshop Outline:

I.What should be in a science abstract?II.How to write a sentence: Characters & ActionsIII.Passive vs. Active voiceIV.How to write a paragraph: Cohesion & CoherenceV.How to write concisely

Page 52: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Concision

Principles of concision:A. Delete words and phrases that mean little or nothing.B. Delete words that repeat the meaning of other words.C. Delete words implied by other words.D. Replace a phrase with a word.E. Change negatives to affirmatives.

Examples:

Ai. Delete words that mean little or nothing:

Kind of actually particular really certain various

Virtually individual basically generally given practically

Productivity actually depends on certain factors that basically involve psychology more than any particular technology.

Page 53: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Concision

Principles of concision:A. Delete words and phrases that mean little or nothing.B. Delete words that repeat the meaning of other words.C. Delete words implied by other words.D. Replace a phrase with a word.E. Change negatives to affirmatives.

Examples:

Ai. Delete words that mean little or nothing:

Kind of actually particular really certain various

Virtually individual basically generally given practically

Productivity actually depends on certain factors that basically involve psychology more than any particular technology.

Change to:Productivity depends on psychology more than on technology.

Page 54: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Aii. Delete phrases that mean little or nothing:

As a matter of fact it should be pointed out I might add thatThe course of it is noteworthy that the fact thatIt is significant that the presence of It is known that

It is interesting to note that over 90 incidents of satellite fragmentations have produced over 36,000 kilograms of space debris.

Page 55: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Aii. Delete phrases that mean little or nothing:

As a matter of fact it should be pointed out I might add thatThe course of it is noteworthy that the fact thatIt is significant that the presence of It is known that

It is interesting to note that over 90 incidents of satellite fragmentations have produced over 36,000 kilograms of space debris.

Change to:More than 90 incidents of satellite fragmentations have produced over 36,000 kilograms of space debris.

From a single journal issue:Studies have revealed thatElegant experimental work provides striking evidence thatThe results gathered so far indicate thatStudies have shown thatWe should also remember thatIt is therefore of great interest several recent reports suggest thatCurrent genetic findings suggest that

Page 56: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

B. Delete words that repeat the meaning of other words:

Full and complete first and foremost any and allTrue and accurate each and every basic and fundamental

C. Delete words implied by other words:

basic fundamentals future plans each individual final outcomevarious different large in size round in shape unusual in naturein an accurate manner Of a strange type of a bright color at an early time

During that period of time, the membrane area became pink in color and shiny in appearance.

Page 57: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

B. Delete words that repeat the meaning of other words:

Full and complete first and foremost any and allTrue and accurate each and every basic and fundamental

C. Delete words implied by other words:

basic fundamentals future plans each individual final outcomevarious different large in size round in shape unusual in naturein an accurate manner Of a strange type of a bright color at an early time

During that period of time, the membrane area became pink in color and shiny in appearance.

Change to:During that period, the membrane became pink and shiny.

Imagine someone trying to learn the rules for playing the game of chess.

Learning implies someone trying; chess is a kind of game.

Change to: Imagine learning the rules of chess.

Page 58: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

D. Replace a phrase with a word:

At this point in time nowAt that point in time thenHas the ability to canIn light of the fact that becauseConcerning the matter of aboutIn the event that ifIn the vicinity of nearIn a situation in which whenIt is possible that mayOwing to the fact that becauseThe question as to whether whetherThere is no doubt but that no doubt

Despite the fact that the data were checked, errors occurred.

Page 59: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

D. Replace a phrase with a word:

At this point in time nowAt that point in time thenHas the ability to canIn light of the fact that becauseConcerning the matter of aboutIn the event that ifIn the vicinity of nearIn a situation in which whenIt is possible that mayOwing to the fact that becauseThe question as to whether whetherThere is no doubt but that no doubt

Despite the fact that the data were checked, errors occurred.

Change to:Although the data were checked, errors occurred.

Page 60: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

This is the most difficult type of redundancy to fix because it requires a large vocabulary:

As you carefully read what you have written to improve wording and catch errors of spelling and punctuation, the thing to do before anything else is to see whether you could use sequences of subjects and verbs instead of the same ideas expressed in nouns.

carefully read what you have written… editthe thing to do before anything else firstuse X instead of Y replacenouns instead of verbs nominalizationssequences of subjects and verbs clauses

Change to:As you edit, first replace nominalizations with clauses

Page 61: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

E. Change negatives to affirmatives:

Expressing ideas in the negative form is less efficient and direct than the affirmative.

Except when applicants have failed to submit applications without complete documentation, benefits will not be denied.

Page 62: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

E. Change negatives to affirmatives:

Expressing ideas in the negative form is less efficient and direct than the affirmative.

Except when applicants have failed to submit applications without complete documentation, benefits will not be denied.

Change to:You will receive benefits only if you submit all of your documents.

Not different similar not many fewNot the same different not often rarelyNot allow prevent not stop continueNot notice overlook not include omit

Page 63: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Excessive Hedging and IntensifyingSome common hedges:Usually Often sometimes almost virtually possiblyPerhaps apparently in some ways somewhat to a certain extent In some respects

Most many some a certain number of

May might can could seem appear suggest indicate

There seems to be some evidence that may suggest that certain differences between Japanese and Western rhetoric could derive from historical influences possibly traceable to Japan’s long cultural isolation and Europe’s equally long history of cross-cultural contacts.

Could be changed to:This evidence proves that Japanese and Western rhetorics differ because of Japan’s long cultural isolation and Europe’s equally long history of cross-cultural contacts.

But might better be changed to:This evidence suggests that aspects of Japanese and Western rhetoric differ because of Japan’s long cultural isolation and Europe’s equally long history of cross-cultural contacts.

Page 64: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Intensifying:Avoid phrases that characterize the truth status of a statement:Clearly, doubtless, undoubtedly, obviouslyas is well-knownit should not be necessary to mentionas you are by now well awareas should be apparent by nowas you have seen from the above

Avoid words that color the qualities of an observation and are not supported by further explanation or definition:magnificent, fascinating, incredible, awesome, terrible, unbelievable, unparallel, exciting, fantastic, bizarre

Avoid efforts to convince the reader by language:The results clearly show thatIt is obvious from Figure 1 thatThe data argue convincingly thatThe only possible interpretation of these results is

If the results are clear, obvious, convincing, etc. the reader does not need to be told these things. Moreover, the use of these terms undermines the significance of results that do not include these terms.

Page 65: Scientific Writing Workshop All are agreed that the articles in our journals-even the journals with the highest possible standards-are, by and large, poorly

Key Principles:

Readers prefer that the main characters are subjects and most of the verbs name the actions of the characters.

Sentences are cohesive with one another when we see at the beginning of a second sentence information that appeared toward the end of the preceding sentence.

Passages are coherent when we see that the topics of each sentence in the passage constitute a relatively small set of related ideas.

Be concise:-Delete words and phrases that: mean little or nothing; that repeat the meaning of other words; that are implied by other words.-Replace a phrase with a word.-Change negatives to affirmatives.

Avoid hedging & intensifying; limit abbreviations