Research Methods in CS Actors and Actions in Scientific Writing.

Research Research Methods in Methods in

CSCSActors and Actions Actors and Actions in Scientific Writingin Scientific Writing

Actors and ActionsActors and Actions

Principles:Principles:

1.1. Put actions in verbsPut actions in verbs

2.2. Put actors in subjectsPut actors in subjects

3.3. Keep subjects near verbsKeep subjects near verbs

Acknowledgement: Acknowledgement:

Slides based mostly on Duke University Graduate School Slides based mostly on Duke University Graduate School Scientific Writing Resource at Scientific Writing Resource at https://cgi.duke.edu/web/sciwriting (Subjects and Actions) (Subjects and Actions)

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Principle 1: Put actions in Principle 1: Put actions in verbsverbs

Nouns are words for things –Nouns are words for things –chair, table chair, table

Verbs are action words – Verbs are action words – to observe, to analyzeto observe, to analyze

Verbs can be turned into nouns – Verbs can be turned into nouns – observation, observation, analysisanalysis• Called Called nominalizationsnominalizations – – concept nounsconcept nouns or or abstract abstract

nounsnouns• Hide action within a thingHide action within a thing

Scientific writers often use Scientific writers often use ““clunkyclunky”” (awkward) (awkward) abstract nouns instead of abstract nouns instead of ““spunkyspunky”” (strong, (strong, interesting) verbsinteresting) verbs• DonDon’’t misuse abstract nouns to convey actiont misuse abstract nouns to convey action

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Put actions into verbsPut actions into verbs

Action Nominalization

to observe observation

to analyze analysis

to occur occurrence

to understand understanding

to investigate investigation

to perform performance

to compile compilation

to execute execution

to allocate allocation

to improve improvement

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Put actions in verbsPut actions in verbs

Readers expect sentenceReaders expect sentence’’s main action in verb s main action in verb (predicate)(predicate)

Scientific writers often use abstract nouns to Scientific writers often use abstract nouns to convey main action, use weak verbsconvey main action, use weak verbs

This disconnects meaning from expected This disconnects meaning from expected structurestructure

Clunky abstract noun; bland, weak verb: Clunky abstract noun; bland, weak verb: We We performedperformed an an analysianalysis on the data.s on the data.

Spunky verb: Spunky verb: We We analyzedanalyzed the data. the data.

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Put actions in verbsPut actions in verbs

Revision technique for sentences:Revision technique for sentences:

Underline all nominalizations Underline all nominalizations (concept/abstract nouns)(concept/abstract nouns)

Should each be changed to verb?Should each be changed to verb?

Alternative technique:Alternative technique:

Underline all verbsUnderline all verbs

Does each verb capture main action of Does each verb capture main action of sentence?sentence?

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Put actions in verbsPut actions in verbs

Nominalizations not always bad – can Nominalizations not always bad – can provide useful link backwards to actionsprovide useful link backwards to actions

We aWe analyzednalyzed the data. This the data. This analysianalysis s demonstrates the need for additional demonstrates the need for additional experiments.experiments.

Summary of Principle 1: Summary of Principle 1:

Use Use ““spunkyspunky”” verbs instead of verbs instead of ““clunkyclunky”” nouns nouns to convey actionto convey action

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Principle 2: Put actors in Principle 2: Put actors in subjectssubjects

Readers expect main actor to be found in sentenceReaders expect main actor to be found in sentence’’s s subjectsubject

✖✖The The analysianalysis of the data from the experiment s of the data from the experiment was was performedperformed by the team by the team’’s statistician s statistician usingusing a suite of a suite of R programs.R programs.

Above uses abstract noun for subject, weak verb, 20 Above uses abstract noun for subject, weak verb, 20 wordswords

✔✔The teamThe team’’s statistician s statistician analyzedanalyzed the data from the the data from the experiment experiment usingusing a suite of R programs a suite of R programs..

Above extracts action from abstract noun, makes Above extracts action from abstract noun, makes main verb, moves actor to subject, 15 wordsmain verb, moves actor to subject, 15 words

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Put actors in subjectsPut actors in subjects

✔✔The teamThe team’’s statistician s statistician analyzed analyzed the data from the data from the experiment using a suite of R programsthe experiment using a suite of R programs..

What about the following alternative?What about the following alternative?

✔✔The team’s statistician The team’s statistician usedused a suite of R a suite of R programs programs to analyze to analyze the data from the the data from the experiment.experiment.

Which is betterWhich is better??

It depends upon whether It depends upon whether ““to use Rto use R”” or or ““to to analyze dataanalyze data”” is more important in the context is more important in the context

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Put actors in subjectsPut actors in subjects

Grammatical subject of sentence answers: What Grammatical subject of sentence answers: What is this sentence about?is this sentence about?

Scientific writing often exhibits Scientific writing often exhibits subject shiftingsubject shifting: : subjects change erratically throughout a subjects change erratically throughout a paragraphparagraph

Subjects should shift only when the topic shiftsSubjects should shift only when the topic shifts

Paragraphs effective when they discussParagraphs effective when they discuss1.1. a single topica single topic

2.2. series of related topics that build logically on one series of related topics that build logically on one anotheranother

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Put actors in subjectsPut actors in subjects

✔✔ To understand human evolution, To understand human evolution, genomes genomes from related primates from related primates are necessary. For are necessary. For example, several example, several primate genomes primate genomes are needed are needed to identify features common to primates or to identify features common to primates or unique to humans. Fortunately, such unique to humans. Fortunately, such genome-genome-wide explorationwide exploration is now a reality; in the past 5 is now a reality; in the past 5 years, years, genome sequences genome sequences of several of several nonhuman primates have been released.nonhuman primates have been released.

Subjects and main actors are Subjects and main actors are ““primate genome primate genome sequencessequences””

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Put actors in subjects Put actors in subjects

✖✖ To understand human evolution, To understand human evolution, genomes from genomes from related primates related primates are necessary. For example, are necessary. For example, identification of featuresidentification of features common among common among primates or unique to humans will require primates or unique to humans will require several primate genomes. Fortunately, several primate genomes. Fortunately, scientists scientists can now do such genome-wide can now do such genome-wide exploration; in the past 5 years, exploration; in the past 5 years, the community the community has released several nonhuman primate has released several nonhuman primate genome sequences.genome sequences.

Above shifts subject twice, disconnecting it from Above shifts subject twice, disconnecting it from the topic of the paragraphthe topic of the paragraph

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Put actors in subjectsPut actors in subjects

✔✔Technology Technology often drives science. Among the most often drives science. Among the most impressive recent technological advances is impressive recent technological advances is DNA DNA sequencingsequencing. . More efficient sequencing More efficient sequencing has reduced has reduced the cost of generating sequence data significantly. the cost of generating sequence data significantly. Cheaper dataCheaper data in turn enables more researchers to in turn enables more researchers to do data-intensive experiments, which results in a do data-intensive experiments, which results in a huge amount of data huge amount of data being released into the public being released into the public domain. domain. Dealing with data Dealing with data in such large quantity in such large quantity will require a new generation of scientists.will require a new generation of scientists.

Subject shifts, but flows logically to make an Subject shifts, but flows logically to make an argumentargument

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Put actors in subjectsPut actors in subjects

Revision technique for paragraph:Revision technique for paragraph:

Highlight subject of each sentenceHighlight subject of each sentence

Does the structure of subjects match Does the structure of subjects match information meant to be conveyed?information meant to be conveyed?a.a. do subjects jump from one thing to another do subjects jump from one thing to another

abruptly? abruptly?

b.b. do subjects shift only when intended topic do subjects shift only when intended topic shifts?shifts?

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Principle 3: Keep subjects Principle 3: Keep subjects near verbs near verbs

Confuses readers if who and what of sentence are far Confuses readers if who and what of sentence are far apartapart

Often caused by long, complex subjects with verb at endOften caused by long, complex subjects with verb at end

Must reparse (reread) sentence to understand it.Must reparse (reread) sentence to understand it.

✖✖Farmers Farmers that understand the difference between the that understand the difference between the soil requirements of plants when they are seedlings and soil requirements of plants when they are seedlings and their requirements when they are mature their requirements when they are mature are in high are in high demademandnd..

✔✔Farmers are in high demand if they can understand the Farmers are in high demand if they can understand the difference between the soil requirements of plants when difference between the soil requirements of plants when they are seedlings and their requirements when they they are seedlings and their requirements when they are mature.are mature.

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Keep subjects near Keep subjects near verbsverbs

Long lists break link between subject and verb, Long lists break link between subject and verb, forcing readers to reparse sentenceforcing readers to reparse sentence Peanuts, shrimp, almonds, milk or anything else with Peanuts, shrimp, almonds, milk or anything else with

lactose, and wheat or anything with gluten all lactose, and wheat or anything with gluten all representrepresent foods that people are commonly allergic to. foods that people are commonly allergic to.

Revise by establishing context before listRevise by establishing context before list People People areare commonly allergic to foods like peanuts, commonly allergic to foods like peanuts,

shrimp, milk or anything else with lactose, and wheat shrimp, milk or anything else with lactose, and wheat or anything else with gluten.or anything else with gluten.

Note: This uses weak Note: This uses weak ““to beto be”” verb, but sentence is verb, but sentence is understandableunderstandable

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Keep subjects near Keep subjects near verbsverbs

Revision technique for sentences:Revision technique for sentences:

Identify the main subject and its verbIdentify the main subject and its verb

If far apart, rephrase sentence to bring If far apart, rephrase sentence to bring closer togethercloser together

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Keep subject near Keep subject near verbsverbs

Consider example sentence:Consider example sentence:✖✖ The TRANSFAC database has been subject to different The TRANSFAC database has been subject to different improvementsimprovements, , modificationsmodifications, and , and extensionsextensions in structure and in structure and content over the years. content over the years.

Uses list of abstract nouns to convey actionUses list of abstract nouns to convey action

Has awkward and meaningless verb Has awkward and meaningless verb ““has been subject tohas been subject to””

Possible revisionPossible revision::✔✔ The TRANSFAC database has been The TRANSFAC database has been improvedimproved, , modifiedmodified, and , and extendedextended in both structure and content over the years. in both structure and content over the years.

Do we need all the verbs? Does Do we need all the verbs? Does improvedimproved imply imply modifiedmodified? ? imply imply extendedextended??

If implied, they are clutter. Cut the clutter!If implied, they are clutter. Cut the clutter!

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Keep subject near Keep subject near verbsverbs

Consider example sentence: Consider example sentence: ✖✖Mapping Mapping of open chromatin regions, post-translational histone of open chromatin regions, post-translational histone modifications and DNA methylation across a whole genome is now modifications and DNA methylation across a whole genome is now feasible, and new non-coding RNAs can be sensitively identified via feasible, and new non-coding RNAs can be sensitively identified via RNA sequencing.RNA sequencing.

Gives list before establishing contextGives list before establishing context

Has main action in nominalization Has main action in nominalization ““mappingmapping””

Possible revison:Possible revison:✔✔ It is now feasible to map open chromatin regions, post-translational It is now feasible to map open chromatin regions, post-translational histone modifications and DNA methylation across a whole genome, histone modifications and DNA methylation across a whole genome, andand to sensitively identify new non-coding RNAs via RNA sequencing. to sensitively identify new non-coding RNAs via RNA sequencing.

Easier to understandEasier to understand

Perhaps break two parts into two sentences (at Perhaps break two parts into two sentences (at andand))

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Keep subject near Keep subject near verbsverbs

Consider example sentence: Consider example sentence: ✖✖Significant positive Significant positive correlations correlations were evident between were evident between the substitution rate and a nucleosome score from the substitution rate and a nucleosome score from resting human T-cells.resting human T-cells.

Has main action in nominalization Has main action in nominalization ““correlationcorrelation””

Intended action probably not Intended action probably not ““were evidentwere evident””

Possible revision:Possible revision:✔✔ In resting human T-cells, the substitution rate In resting human T-cells, the substitution rate correlated with a nucleosome score.correlated with a nucleosome score.

Perhaps add Perhaps add ““positivelypositively”” after after ““correlatedcorrelated””

Straightforward, shorterStraightforward, shorter

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Keep subject near Keep subject near verbsverbs

Consider example sentence: Consider example sentence: ✖✖The The possibilitypossibility that some termini have a base composition that some termini have a base composition different from that of DNA simply because they are the different from that of DNA simply because they are the nearest neighbors of termini specifically recognized by the nearest neighbors of termini specifically recognized by the enzymes enzymes can be checkedcan be checked by comparing the experimental by comparing the experimental results with those expected from the nearest neighbor data. results with those expected from the nearest neighbor data.

Extreme case of subject verb separationExtreme case of subject verb separation

Revision to bring Revision to bring possibilitypossibility and and checkedchecked nearer nearer✔✔ If we compare the experimental results with those If we compare the experimental results with those expected from the nearest neighbor data, we can check the expected from the nearest neighbor data, we can check the possibility that some termini have a base composition possibility that some termini have a base composition different from that of DNA simply because they are the different from that of DNA simply because they are the nearest neighbors of termini specifically recognized by the nearest neighbors of termini specifically recognized by the enzymes.enzymes.

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Keep subject near Keep subject near verbsverbs

First revision (repeated from previous slide):First revision (repeated from previous slide):✔✔ If we compare the experimental results with those If we compare the experimental results with those expected from the nearest neighbor data, we can expected from the nearest neighbor data, we can check the possibility that some termini have a base check the possibility that some termini have a base composition different from that of DNA simply composition different from that of DNA simply because they are the nearest neighbors of termini because they are the nearest neighbors of termini specifically recognized by the enzymes.specifically recognized by the enzymes.

Second revision:Second revision:✔✔If we compare our expectations with experimental If we compare our expectations with experimental results, we identify any termini that differ in base results, we identify any termini that differ in base composition simply because they are the nearest composition simply because they are the nearest neighbors of those specifically recognized by the neighbors of those specifically recognized by the enzymes.enzymes.

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