Chapter 5 Structuring Sentences

5.1 Key Insights

Now that we move onto structuring meaningful sentences, in addition to the key principles introduced thus far, we will see that … Scientific writing is:

Considerate Information within a sentence is structured according to the reader’s expectations.

5.2 Sentence Types

5.2.1 Simple Sentences

Simple sentences contain a single independent clause. Some definitions:

• A clause is the mental is a group of words containing a subject and a predicate (the verb or verb phrase) and may include direct or indirect objects.

• An independent clause contains a verb and subject but doesn’t begin with a subordinating word or phrase (e.g. because or while).

• A dependent clause starts with a subordinating word or phrase (e.g. because or while) and can’t stand alone as a sentence because it does not represent a complete thought.

Example 5.1 (Simple Sentences) 👍 The microbiota plays an important role in the health of boiler chickens.

5.2.2 Compound Sentences

• Composed of at least two independent clauses, but no dependent clauses.
• Clauses can be joined by:
• A comma plus a coordinating conjunction (“…, for/and/nor/but/or/yet/so”)
  • Remember the 7 coordinating conjunctions with the acronym FAN BOYS.
• A semi-colon alone (“…; …”)

Example 5.2 (Compound Sentences) 👍 The microbiota plays an important role in the health of boiler chickens, so it is a topic of intense research.

👍 The microbiota plays an important role in the health of boiler chickens; it is a topic of intense research.

5.2.3 Complex Sentences

• Composed of one independent clause, and one or more dependent clauses.
• A dependent clause must always be connected with an independent clause.
• Dependent clauses can be inserted in the middle of the sentence, or added to the end using:
  • commas (“…, …”)
  • em dashes (“… — …”)

Don’t mistake em dashes with hyphens and en dashes! Table 5.1 makes the distinction clear.

Table 5.1: Hyphenation and dashes. The choice of using spaces before and after en and em dashes is dictated by your style guide — rules will vary.

Punctuation	Name	Purpose	Example
-	Hyphen	Compound nouns	High-throughput sequencing
–	En-dash	“Through”	4 – 6 hours
—	Em-dash	Strong break	Various uses

Subordinating conjunctions (see table 5.2) are key to building complex sentences.

Table 5.2: Subordinating conjunctions.

after	once	until
although	provided that	when
as	rather than	whenever
because	since	where
before	so that	whereas
even if	than	wherever
even though	that	whether
if	though	while
in order that	unless	why

Example 5.3 (Complex Sentences) 👍 The microbiota is a topic of intense research, since it plays an important role in the health of boiler chickens.

👍 The microbiota, a topic of intense research, plays an important role in the health of boiler chickens.

👍 The microbiota — a topic of intense research — plays an important role in the health of boiler chickens.

Example 5.4 (Em dashes) The em dash is a hard stop, so use it to introduce important or dramatic information in the middle or end of a sentence. In this case it’s a bit too dramatic.

👎 The microbiota — the microflora in the gastrointestinal tract — plays an important role in the health of boiler chickens.

👍 Knowledge on the human microbiota is mainly motivated by its adverse effect on health — it is implicated in obesity.

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It’s also what you’ll find in titles:

👍 Intestinal microbiota and metabolites — Implications for broiler chicken health and performance

Parentheses let the reader know they can safely skip over this information. It’s information that is good to know, but may not be really crucial — maybe they even know it already. It’s why information like references appear here. The exception may be acronyms, which typically appear in parentheses but are important if the reader didn’t already know them.

Example 5.5 (Parentheses) 👍 The microbiota (the microflora in the gastrointestinal tract) plays an important role in the health of boiler chickens.

5.2.4 Combination Sentences: Compound & Complex

• A combination of compound and complex sentences.

Example 5.6 (Combination Sentences: Compound & Complex) 👍 The microbiota, the microflora in the gastrointestinal tract, is a topic of intense research, because it plays an important role in the health of boiler chickens.

5.2.5 Problem Words: That and Which

That and which are frequently used to add secondary clauses — but they are frequently confused!

• That is the restrictive, defining, pronoun
• Which is the non-restrictive, non-defining, pronoun.

Keep these 2 points in mind:

1. Which phrases don’t change the meaning of the sentence when excluded.
2. Which phrases introduce an aside, or by-the-way, type of information.

Example 5.7 (That versus Which) 👍 Fish that live in caves display many adaptations to living in darkness.

That in the first sentence restricts the statement to cave-dwelling fish: “Among all the fish of the world, some live in caves. Those that live in caves have many adaptations to living in darkness.”

👎 Fish, which live in caves, display many adaptations to living in darkness.

By using which, the second sentence states: “All fish live in caves and have many adaptations to living in darkness”.

👍 Astyanax fish, which live in caves, display many adaptations to living in darkness.

The last sentence illustrates how to use which to introduce information in a “by-the-way” manner.

Example 5.8 (That, Which, or an Em dash) When which (or whom) have a preposition, the preposition can come at the beginning of the clause…:

👍 The Healthy Eating Index-2010 (HEI-2010), with which we evaluated diet, is the gold-standard.

…or at the end of the clause:

👍 The Healthy Eating Index-2010 (HEI-2010), which we evaluated diet with, is the gold-standard.

Use that at beginning of the clause…:

👍 The Healthy Eating Index-2010 (HEI-2010) that we evaluated diet with is the gold-standard.

… or highlight the information with an em dash:

👍 We evaluated diet using the gold-standard — The Healthy Eating Index, 2010 (HEI-2010).

Table 5.3: Distinguish between who, that, and which given the item referred to.

Subject	Object	Items
who	who(m)	People
that	that	People or Things
which	which	Things

5.2.6 Streamline Subject-Verb-Object Sentences

In English, readers expect a grammatical subject to be followed immediately by a verb. Complex and combination sentences (see above) encourage creative structures, where intervening material can be introduced between the subject and verb. As this material gets longer, it’s more likely that it contains important information that is not being properly emphasized. Therefore, streamline sentences by removing gaps that interrupt a subject-verb-object structure.

The reader will naturally ask if the intervening material between the subject and verb is important. You must make the purpose of the material clear for the reader: Is it important or is it a tangent?

There are two ways to close the subject-verb gap. If the material is important, you can place it in a separate sentence or re-position it at the beginning or end of the sentence to aide in flow. Alternatively, if the material is not important, delete it.

Example 5.9 (Close the Subject-Verb Gap by Processing Intervening Material) This example sentence obstructs the reader because the grammatical subject, ravens, is separated from the verb phrase, live in by 14 words.

👎 Ravens, a species of bird that regularly engages in complex social behaviour such as deception, live in non-breeding flocks for the first year of their lives.

If the intervening material is important, it can be emphasised by splitting the sentence in two.

👍 Ravens are a species of bird that regularly engages in complex social behaviour such as deception. They live in non-breeding flocks for the first year of their lives.

If the intervening material is not important it can be deleted.

👍 Ravens live in non-breeding flocks for the first year of their lives.

Intervening material between the verb and object can also disrupts reading flow. Place this material either at the beginning or at the end of the sentence.

Example 5.10 (Close the Verb-Object Gap by Rearrangement) In this example, there is a 13-word gap between the verb (“tested”) and the object (“ability”). This gap can be closed in two ways.

👎 Ravens were tested, using a series of pre-recorded calls from familiar and unfamiliar birds, for their ability to remember former group members.

One way is to place the intervening material at the beginning of the sentence, emphasising the main clause by placing it in the end (stress position) of the sentence.

👍 Using a series of pre-recorded calls from familiar and unfamiliar birds, ravens were tested for their ability to remember former group members.

Alternatively the intervening material can be placed at the end of the sentence. This approach places less emphasis on the main clause.

👍 Ravens were tested for their ability to remember former group members using a series of pre-recorded calls from familiar and unfamiliar birds.

A more subtle method of closing the subject-verb gap is to make the topic of the sentence the grammatical subject of the sentence. To do this, first find the main topic of the sentence, then express the topic’s actions as verbs.

Example 5.11 (Close the Subject-Verb Gap by Redefining the Grammatical Subject) In the first sentence, there is a 9-word gap between the grammatical subject (“decline”) and the verb (“occurred”). The topic (“dissolved oxygen concentration”) is not the grammatical subject, and the action (“decline”) is a buried verb.

👎 A substantial decline of dissolved oxygen concentration in European river water has occurred since 1900.

In the second sentence, the writer has made the topic of the sentence into its grammatical subject, connecting subject and verb.

👍 Dissolved oxygen concentration has declined substantially in European river water since 1900.

5.2.7 Active & Passive Voice: Use Word Order to Reflect Context

Now that we have an idea of how to construct sentences, we can begin by deciding what is important (to be stressed), less important (to be subordinated), and not important (to be omitted). Next, take the reader’s expectations into account, by considering the position of each word. The following table describes the most important positions in a sentence in line with reader expectations.

Topic Position	Stress Position
Start	End
Old information	New information
Familiar	Complex
Short	Long

The following sentences contain the same facts, but differ in focus. Due to this, they have to be written in either an active or a passive voice. Here, the choice, i.e. the word order, is determined by context, not by convention to use only one voice and not the other.

In the active voice, the subject performs the action. The subject is sand flies, the verb is carry, and the object is Leishmania parasites. Our attention is on sand flies. The sentence emphasises that they carry Leishmania parasites (as distinct from carrying e.g. microsporidia). We would use this sentence if the previous discussion was about sand flies.

Example 5.12 (Active voice) 👍 Sand flies carry Leishmania parasites.

In the passive voice, the subject receives the action. The subject is Leishmania parasites, the verb phrase is are carried by, and the object is sand flies. Our attention is on the Leishmania parasites. The sentence emphasises that they are carried by sand flies (as distinct from being carried by e.g. fleas). We would use this sentence if the previous discussion was about Leishmania parasites.

Example 5.13 (Passive voice) 👍 Leishmania parasites are carried by sand flies.

5.2.8 Use the Active and Passive Voices Appropriately

Aside from allowing word order to dictate active versus passive voice, there are specific cases when we want to use one versus the other.

Example 5.14 (Use the active voice to claim ownership) Remember, in an active voice sentence, the subject performs the action. The active voice states who or what performed an action. In a passive voice sentence, the subject receives the action.

👎 Considering the robust enrichment for metabolic kinases, a substantial reprogramming of metabolism upon macrophage activation was hypothesized.

👍 Considering the robust enrichment for metabolic kinases we hypothesized a substantial reprogramming of metabolism upon macrophage activation.

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👎 It was hypothesized that the changes in profiles of fatty acids may serve as a mechanism for improved cognition.

👍 We hypothesized that the changes in profiles of fatty acids may serve as a mechanism for improved cognition.

Some advantages of the active voice, which is gaining in popularity in scientific literature:

• Avoids false modesty
• Projects enthusiasm
• Enlivens your writing
• Allows you to claim ownership of results

Don’t be afraid to state the agent of an action even if it is I or we when appropriate. However, when using the active voice, the agent is not always human, as shown in the following examples.

Example 5.15 (The Active and Passive Voices) In an active voice sentence, the subject performs the action. In a passive voice sentence, the subject receives the action.

👍 Macrophages generate nitric oxide metabolites during the immune response. Active voice

👍 Nitric oxide metabolites are generated by macrophages during the immune response. Passive voice

In the Results section, first person pronouns (I and we) can be used with verbs in the active voice to take ownership of a result.

Example 5.16 (Use Active Voice when Reporting Results) In these sentences from a Results section, the active voice is more effective.

👎 Isolated mitochondria were assayed for nitric oxide synthase activity. Passive voice

👍 We assayed isolated mitochondria for nitric oxide synthase activity. Active voice

We already saw that the choice of word location and placement in a paper can determine the choice of active or passive voice. Another consideration is style, changing the voice of a sentence can make it more concise and readable.

Example 5.17 (Active Versus Passive Voice Determined by Style) This sentence comes from a Results section, in which the active voice is often preferable. The passive form is not only longer, but also contains a buried verb. Can you find it?

👎 The action potential of ventricular myocardial fibres was determined by direct measurement.Passive voice

👍 We directly measured the action potential of ventricular myocardial fibres. Active voice

The passive voice allows the author to distance himself from his own work, thus facilitating an unbiased viewpoint. However, excessive use of the passive voice leads to dull and dense writing. It can be used effectively in certain situations as shown in the margin note.

Some advantages of the passive voice include:

• Author remains anonymous
• More objectivity and modesty
• Shorten subject length

Note that the passive voice is appropriate in the Materials & Methods section. This is useful if the work described was performed by technicians or third party service providers who are not authors. Moreover, using the passive voice in the Materials & Methods section focuses the action on the topic of interest.

Example 5.18 (Use Passive Voice when Reporting Materials & Methods) In this sentence from a Materials & Methods section, the topic is cells. Using the passive voice emphasises the specific topic.

👎 We incubated the cells at room temperature for two days.Active voice

👍 The cells were incubated at room temperature for two days. Passive voice

Exercise 5.1 (Passive versus Active Voice) Complete the following three tasks for each of the sentences below:

• Identify if it is written in the active or passive voice
• Consider if this sentence should be re-written in the other voice. Why or why not?
• Think about where this sentence would appear in a research article. What purpose does it serve?

• If you think it should be re-written, do so in the space provided.

• Betaine was administered to rats orally through a syringe fitted with a ball-type feeding needle in a volume of 0.2 ml per rat per feeding.

• When lithium was administered to rats prior to sacrifice, renal GSH level, but not hepatic GSH level, was increased significantly.

5.2.9 Clause Order Influences Your Message

Let’s return to the topic and stress positions of a sentence. Once you decide what the message of a sentence is, you can construct it to ensure that readers interpret the message as you intended by taking advantage of the fact that the end (stress position) of the sentence and the main independent clause are emphasized more than the beginning (topic position) of the sentence and the dependent clause.

Example 5.19 (Use Clause Order to Influence Your Message) The sentences in table 5.4 convey exactly the same information, but generate different reader interpretations. For the reader, the take home message of these sentences is highly dependent on the sentence structure. Readers of the first sentence are the least likely to interpret the sentence as recommending PPIs. Conversely, readers of the last sentence are the most likely to interpret the sentence as a recommendation of PPIs.

Table 5.4: For each sentence, the main clause is shown in italics.

Example Sentence	Information in Main Clause	Position of Main Clause	Reader’s Perception of PPIs
Although Proton Pump Inhibitors (PPIs) relieve the symptoms of stomach ulcers, they may increase the risk of bone fractures.	Negative	End	Mostly Bad
Proton Pump Inhibitors (PPIs) relieve the symptoms of stomach ulcers, but they may increase the risk of bone fractures.	Positive	Start	Generally Bad
Proton Pump Inhibitors (PPIs) may increase the risk of bone fractures, but PPIs relieve the symptoms of stomach ulcers.	Negative	Start	Generally Good
Although taking Proton Pump Inhibitors (PPIs) may increase the risk of bone fractures, PPIs relieve the symptoms of stomach ulcers.	Positive	End	Mostly Good

Exercise 5.2 (Clause placement) Here are four sentences taken from the Discussion section of a paper proposing a new alternative to a standard, commonly-used protocol. Underline the main clause of each sentence and order them from weakest (A) to strongest (D) criticism of the standard protocol.

• The standard protocol suffers from several drawbacks, but it is simple to perform.
• Although the standard protocol suffers from several drawbacks, it is simple to perform.
• The standard protocol is simple to perform, but it suffers from several drawbacks.
• Although the standard protocol is simple to perform, it suffers from several drawbacks.

5.2.10 Position the Sentence Topic Appropriately

The sentence topic is clearly stated in well-composed sentences. If the topic appears only after a long preamble of several words, the reader has difficulty identifying it. Aim to state the topic as soon as possible.

Example 5.20 (State the Topic at the Beginning of the Sentence) The first sentence begins with a long preamble before stating the topic. It has less impact than the second.

👎 Due to the small sample size and the presence of several confounding variables, the statistical power of the test was reduced.

👍 The statistical power of the test was reduced due to the small sample size and the presence of several confounding variables.

Alternatively, attention can be drawn to the topic of the sentence by focusing the action of the sentence on it.

Example 5.21 (Focus action on topic of the sentence) The topic of all three sentences is the relatedness of humans and chimpanzees. The first sentence is unfocused because the topic is located in the dependent clause (after the comma).

👎 There is a high degree of DNA sequence identity between the human and chimpanzee genomes, which illustrates the close relatedness of these species.

An improvement focuses action on the topic by using the passive voice and making it the grammatical subject.

👍 The close relatedness of human and chimpanzee is illustrated by the high degree of DNA sequence identity between their genomes.

However, another possibility would be to use the active voice and make the topic the grammatical object. This works well, despite placing the topic at the end of the sentence. The choice depends on the specific context of the sentence.

👍 The high degree of DNA sequence identity between the human and chimpanzee genomes illustrates the close relatedness of these species.

Exercise 5.3 (Optimal word order) If necessary, rearrange the elements in these sentences into the clearest order for the reader. Use punctuation where necessary.

• Among the factors which influence X / particularly important / are P and Q.

• This was associated / in the USA / with changes in the environment.

• However / only / for some Xs / this operation is defined.

• From now on / since the two cases are almost identical / we will only refer to the first case.

• With each operation / is associated / a number / which refers to the ranking.

• At any time / it is possible to put / on hold / the application / by doing X.

• It is thus possible / to select / from the database / only useful data.

• Important parameters / are / both X and Y.

5.3 Scientific Writing is Clear

5.3.1 Use Transitions Within Sentences

Present lists in a way that is easy for the reader to understand. You can announce the number of items in the list and use the following key transition words:

Transition phrases for presenting lists within sentences:

• i)…., ii)…., iii)….
• … and … , respectively.

Among sentences and even paragraphs, you can use:

• First…, second…, third…

Example 5.22 (Highlight Important Lists) In the first sentence, the reader has to keep track of the three conditions. Announcing how many conditions will be considered and numbering them makes the list’s contents explicit to the reader.

👎 Animals were randomly assigned to the ventilation conditions NAVA, noisy PSV or PCV and ventilated over 24 hours.

A further step is to have the list end the sentence, so it is clear that the parameter (24 hours) is applied to all conditions and not just the third.

👍 Animals were randomly assigned to one of three ventilation conditions for 24 hours: (i) NAVA, (ii) noisy PSV, or (iii) PCV.

When highlighting a one-to-one relationship between the elements of two lists use respectively at the end of the sentence.

Example 5.23 (Make Relationships Between Lists Clear) In the first sentence, there is a one-to-one relationship between the quantitative list and the country list.

👍 Between 1980 and 2010, the per capita consumption of refined sucrose in Canada, Ireland and Germany, decreased by 23%, 20% and 10%, respectively.

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Here, CD47 expression was measured at the mRNA level (but not at the protein level), whereas TSP1 expression was measured at the protein level (but not at the mRNA level).

In the last sentence, the expression of both CD47 and TSP1 is determined at both the mRNA and protein levels.

👍 We determined retinal expression of CD47 and TSP1 at the mRNA and protein level, respectively.

👍 We determined retinal expression of CD47 and TSP1 at the mRNA and protein level.

When listing two points, instead of simply using and, emphasise the items using the following transition words:

Transition words for emphasising two points:

• both … and …_
• Not only …, but also …
• Neither … nor …_
• either … or …

Example 5.24 (Emphasise Key Points) Using both … and places more emphasis on the two items than simply using and

👎 Our results demonstrate that beekeepers must consider pesticide regimens of their target field and those of neighbouring fields that may contribute to pesticide drift.

👍 Our results demonstrate that beekeepers must consider pesticide regimens of both their target field and those of neighbouring fields that may contribute to pesticide drift.

👍 Our results demonstrate that beekeepers must not only consider pesticide regimens of their target field, but also those of neighbouring fields that may contribute to pesticide drift.

The two items are emphasised further by using not only … but also.

Lists containing multiple ands can be very confusing when it becomes ambiguous which items should be paired together. Use these transition words to break up “and pile-ups”.

Transition words for avoiding and pile-ups:

• …, in addition to …
• …, as well as …
  
• …, along with…
• …, together with…

Example 5.25 (Avoid confusion caused by and pile-ups) In this sentence, it appears as if all four parameters belong to foraging speed, until the reader encounters the second feature measured, “extracellular slime”, at the end of the sentence.

Some of the confusion can be helped by stating the measures and then their parameters, but this is still not optimal for the reader.

Using … in addition to … clearly separates the list into two parts.

👎 Measurements included foraging speed and efficiency and composition and amount of extracellular slime.

👎 Measurements included foraging speed and efficiency and extracellular slime composition and amount.

👍 Measurements included foraging speed and efficiency, in addition to extracellular slime composition and amount.

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Using … along with … clearly separates the list into two parts.

👎 We identified A and B as loci highly associated with bipolar disorder and two other regions encompassing known schizophrenia-related genes.

👍 We identified A and B as loci highly associated with bipolar disorder, along with two other regions encompassing known schizophrenia-related genes.

Exercise 5.4 (Ambiguous phrasing) Improper punctuation and word order or choice can cause confusion and ambiguity. Rewrite the following sentences to remove ambiguity. These first two are not academic sentences, but are two great examples nonetheless. What do you think is the correct punctuation?

• Let’s eat grandma.

• Man eating fish.

• We prefer probing cells.

• To obtain red colours, insects and plant roots were used by indigenous people.

• We also demonstrated that x does not equal y as suggested by Walker.

• The European Union (EU) adopted various measures to compare these phenomena. This resulted in smog and pollution levels reduction.