22 Building Paragraphs
22.1 Key Insights
Moving onto paragraphs, we note that, in addition to contextual, concise, clear, correct and considerate, scientific writing is:
Cohesive Sentences are connected with appropriate transitions and in a meaningful order. Consistent Names and the order of information do not change unnecessarily.
Paragraphs are the central unit of currency in scientific writing; they are self-contained, stand-alone arguments. A paragraph can be thought of as representing an uninterrupted train of thought.
22.2 Organisation
Guide the reader through the paragraph by signalling each element in advance and anticipate the reader’s expectations. In general, the topic sentence states your argument, the rest of the paragraph makes your argument. To help the writing process, use the headings from your manuscript outline as topic sentences for paragraphs. Conversely, this should allow the reader to gain a broad understanding of the paper just by reading the topic sentences.
22.2.1 Topic Sentence
The topic and message of the paragraph are stated at the outset. This tells the reader what to expect from the paragraph. In general, you will have only one key message per paragraph.
22.2.2 Details
The sentences following the topic sentence present readers with the details of your argument. Every sentence in a paragraph should relate to the topic sentence, providing new information and building on the previous sentence. In general, details that support the paragraph’s line of argument are given first. Details may also be given in increasing or decreasing order of importance, depending on the purpose of the paragraph and its relation to the text as a whole.
Since a paragraph is a stand-alone unit, previously presented information needs to be restated. Therefore, don’t begin a paragraph with “However, …” or “In addition, …”. Instead, make it obvious how the paragraph relates to preceding paragraphs using phrases such as “In support of the above arguments …”.
Supporting details are followed by contradictory material, which should be introduced with a transition word.
As a rule of thumb, there should be a maximum of one change of direction in the line of argument (e.g. a maximum of one however) per paragraph.
Building understandable paragraphs requires a flow of information. Missing details disrupt this flow and make the text difficult for the reader to understand. Out of place information also interrupts the flow, so be sure that only information relevant to the topic sentence is stated. The reader must be able to follow the logic of the arguments presented in the paragraph.
22.2.3 Concluding Sentence
Paragraphs may benefit from a concluding sentence, particularly when they are lengthy. This restates the central message in a different way and also transitions into the next paragraph by prompting the next topic.
22.3 Scientific Writing is Cohesive — Structure
We first encounter the concept of cohesion in the two basic types of paragraph structure: the _Links-in-a-chain} structure and _Fixed Perspective}. In practice many paragraphs are a mixture of both styles.
22.3.1 Links-in-a-chain Paragraph Structure
In the Links-in-a-chain approach, the object of each sentence is used as the grammatical subject that begins the next sentence. Thus, new information introduced at the end of a sentence becomes the old information in the next, and so on.
```{example, name=“Links-in-a-chain Paragraph Structure”}
We studied human populations inhabiting high-altitude environments. High-altitude environments expose inhabitants to hypoxia. Hypoxia occurs as a result of breathing low- oxygen-content air. As a consequence, high-altitude environments such as the Tibetan Plateau, the Andean Altiplano, and the Ethiopian Highlands are all sparsely populated.
### Fixed Perspective Paragraph Structure
The Fixed Perspective approach allows the subject of the topic sentence to determine the point-of-view of all following sentences. The subject, its synonyms, or its pronouns, are repeated as subjects throughout the paragraph, maintaining a fixed perspective. Therefore, in each sentence a reverse-link is made to the starting, topic sentence.
Remember that repeating the same key words and phrases throughout a paragraph, and the paper, is a powerful way to achieve cohesion and flow. You might be tempted to use a broader vocabulary for variety, but only do so if this does not introduce confusion, inaccuracy or clutter. Decide on the key terms for your study and avoid substituting them with other similar words or even with exact synonyms.
The subject of the topic sentence should be a key term. Key terms include technical words, such as a gene, biological process, or disease, or non-technical words, such as a descriptor or a change of state. Whatever key term is used, it represents the most important concept of the paragraph and should be repeated in a way that clearly links it to the topic sentence.
```{example, name="Fixed Perspective Paragraph Structure"}
_Hemoglobin_ is an oxygen-transporting metalloprotein. _It_ is found in the red blood cells of all but one vertebrate family studied so far. In mammals, _this protein_ alone accounts for about 97% of red blood cell dry mass. In human, _hemoglobin_ is a tetramer, consisting of two α and two β subunits. High hemoglobin concentration reduces hypoxic stress in high-altitude environments.
22.3.2 The Mixed Structure
In reality, paragraphs are frequently built using a combination of both the above techniques.
```{example, name=“The Mixed Paragraph Structure”}
Two known physiological adaptations to high-altitude environments involve hemoglobin. The first is an elevated hemoglobin concentration. The highest concentration known is in the Andean population. The Andean population exhibits a high heritability (\(H^2\) = 0.89) for this trait. The second adaptation is an elevated level of oxygen saturation in the blood. Strikingly, high oxygen saturation is associated with a doubling of neonate survival in Tibet compared to normal oxygen saturation levels.
So far we've seen how structure makes scientific writing cohesive, another important aspect is uing transitions.
## Scientific Writing is Cohesive --- Transitions {#cohesiveTransitions}
### Vary Sentence Length
In the last chapter we saw how to construct sentences. We also noted that shorter is better, as echoed in the principle of being *concise*. In general, longer sentences are more difficult to understand --- they are also more difficult to follow. When sentence lengths increase, the readability of articles suffers. For scientific articles, which are often not very readable, the average sentence length is more than 30 words. For newspaper articles, which are highly readable, it is only 15-20 words. Aim for an average sentence length of about 20 words.
Short single-clause sentences have more impact. Readers assign more importance to short stand-alone sentences and less importance to long sentences of secondary clauses, which are dependent on a main clause.
```{example, name="Break up Long Sentences"}
This sentence only has 42 words. Nonetheless, it can overwhelm the reader with too much information.
👎 Genetic modification of plant foods, including already-available staples such as soybean, maize and rice, is used to express novel and desirable traits by introducing specific, naturally-occurring or synthetic genetic-material, thereby offering some advantage for the producer or the consumer over conventional crops. _(42 words)_
There are three points the author is trying to make:
- GM plants are already available.
- The goal of GM.
- How the goal is achieved.
Each point is stated in an individual sentence in the revision.
👍 Many genetically-modified plants, including staples such as soybean, maize and rice, are already available to consumers. _(16 words)_ words_Genetic modification attempts to express novel and desirable traits, which offer an advantage for the producer or the consumer over conventional crops. _(22)_ This goal is achieved by introducing specific, naturally-occurring or synthetic genetic material, into different species of plants. _(17, 55 total)_
```{exercise, name=“Dividing up long sentences”}
In the simplest case scenario you can split up sentences using punctuation alone. However, there are many ways to deal with very long sentences. Re-write each of the following into shorter sentences.
Using automatic translation software (e.g. Google Translate, Babelfish, and Systran) can considerably ease the work of researchers when they need to translate documents thus saving them money (for example the fee they might have otherwise had to pay to a professional translator) and increasing the amount of time they have to spend in the laboratory rather than at the computer. (60 words)
In order to establish a relationship between document length and level of bureaucracy in European countries and to confirm whether documents, such as reports regarding legislative and administrative issues, vary substantially in length from one language to another, we conducted an analysis of A, B and C. (47 words)
The aim of our study was to assess changes in the level of tolerance of natives of one country towards immigrants over the course of a 50-year period in order to be able to advise governmental agencies on how to develop strategies based on those countries that have been more successful in reducing racism as already investigated in previous studies, but not in such a systematic way, and to establish correlations with data from the USA, which until now have been reported only sporadically. (84 words)
Monolithic sorbent tip technology has proved to be efficient in removing interferences from copper and mercury salts, but it has not been tested for other materials and the recovery of proteinaceous material is often too small, giving rise to analysis problems. (41 words)
Our results show that the performance of the system, in terms of throughput and delay, depends on several factors including the frame duration, the mechanisms for requesting uplink bandwidth, the load partitioning, i.e. the way traffic is distributed, connections, and traffic sources within each connection. (45 words)
Combining sentences can help you link two pieces of information together more closely than if they were in separate sentences. It can also aid you in reducing word count, which is particularly important in the Abstract.
```{example, name="Combining Sentences"}
In this case, the experiment's rationale and the method are combined in one sentence.
👎 We asked whether ... . To answer this question, we analysed ...
👍 To determine whether ..., we analysed ...
---
By combining these two sentences the word count has been reduced by 7 words.
👎 We studied pulmonary artery pressure over the course of 3 hours. We found that pulmonary artery pressure rose to 150% of baseline and remained elevated throughout the experiment. _(28 words)_
👍 We found that pulmonary artery pressure rose to 150% of baseline and remained elevated for the 3-hour duration of the experiment. _(21 words)_
Start paragraphs and sections with shorter sentences to highlight the main topic of the paragraph/section. The final sentence of a paragraph is also usually short. Intervening sentences in the paragraph are longer.
By varying sentence length, you can hold the reader’s interest. Paragraphs with variable sentence lengths are easier to understand because they mimic speech patterns.
22.3.3 Transitions Between Sentences
A paragraph’s flow is built by linking sentences together. Use the following transitions to signal to the reader and build the storyline of each paragraph.
Transition phrases between sentences are most effective when used at the beginning of a sentence, acting as signals for the reader.
| Type | Example | |
|---|---|---|
| Addition | Again, … | Furthermore, … |
| Moreover, … | Further experiments … | |
| Further … | In addition … | |
| Besides X, … | We also note … | |
| Indeed, … | Also, … | |
| Comparison | Likewise | As seen in … |
| When compared to …\(^1\) | Comparing … to …\(^1\) | |
| Similarly, … | In the same way, … | |
| As reported by … | ||
| Contrast | But … | Still … |
| Nevertheless …\(^2\) | Nonetheless …\(^2\) | |
| Instead … | Occasionally … | |
| Unlike …, … | Although … | |
| Of course … | Otherwise … | |
| However, … | Yet … | |
| Despite this …\(^3\) | In contrast, …\(^4\) | |
| On the contrary, …… | In comparison with …\(^1\) | |
| On the other hand … | In reality … | |
| Whereas, … | Conversely … | |
| Emphasis\(^5\) | Notably, …\(^6\) | Interestingly, …\(^6\) |
| Even …\(^7\) | In other words, …\(^8\) | |
| i.e. …\(^{8,9}\) | Strikingly, … | |
| Specifically, … | Importantly, … | |
| Surprisingly, … | ||
| Example | For example, … | This is illustrated by … |
| An example of …, … | Specifically, … | |
| This is exemplified by … | For instance, … | |
| In particular, … | e.g. …\(^8\) | |
| Result, explanation | Therefore, … | Hence, … |
| logical progression | Thus, … | Consequently, … |
| Accordingly, … | Subsequently, … | |
| Here, … | Because of …, … | |
| As a result of … | Because … is … | |
| In this experiment, … | In this case, … | |
| Purpose | For this purpose, … | To this end, … |
| The purpose of X was to … | For the purpose, … | |
| To determine XYZ, we … | ||
| Sequence, time | After … | First, … |
| Later … | Meanwhile, … | |
| Now … | While, … | |
| Subsequently, … | Finally, … | |
| Next, … | Then … | |
| Second, … | Last | |
| During … | When | |
| Start a sentence | To date, … | Currently, … |
| Thus far, … | At present, …\(^{11}\) | |
| End of a sentence | … as yet | … until now |
| … so far | ||
| Summary, Conclusion | Briefly, … | In fact, … |
| To summarise, … | To conclude, … | |
| In summary, … | In conclusion, … | |
| In short, … | Taken together, … |
\(^1\)Note the difference between compare with, emphasising differences between similar classes, e.g. compare Berlin with Paris (Berlin and Paris are both cities, what sets them apart?) and compare to emphasising similarities between different classes, e.g. compare thee to a summer’s day (people and the weather are different classes).
\(^2\)Nevertheless and nonetheless are synonymous, but nonetheless is a more recent term and is gaining in popularity, whereas nevertheless has a long history and its popularity is declining.
\(^3\)Use despite instead of in spite of.
\(^4\)In contrast is a strong transition and can be combined with an emphasising word, such as strong, striking, sharp or stark.
\(^5\)Avoid using: Clearly, Obviously, or Unexpectedly
\(^6\)Both notably and interestingly are more concise alternatives to it is interesting to note that.
\(^7\)Even is used to introduce an extreme case, e.g. Even after 20 years of research….
\(^8\)In other words and i.e. allow key information to be repeated in a different way, thereby adding emphasis.
\(^9\)Use i.e. in the middle (not at the beginning) of a sentence, and don’t confuse it with e.g.
\(^{10}\)Avoid starting a sentence with So….
\(^{11}\)Use at present instead of presently, which literally means soon, not shortly.
```{exercise, name=“Transitions”}
Connect the following three sentence pairs with suitable transition words:
We sampled the transcriptome of CD4 cells using >1 million RNA Seq reads. We did not detect any additional alternative transcripts of yfg1.
We determined whether the increased endotoxin susceptibility of AUF1\(^{-/-}\) mice is due to deregulation of pro-inflammatory cytokine expression. We measured the serum TNF\(\alpha\) level in AUF1\(^{-/-}\) mice after LPS challenge.
This new gene is closely related to the fms family. The gene was designated flt (fms-like tyrosine kinase).
```{exercise, name="Type of information"}
Transitions can be used to add neutral, positive or negative information. Consider the sentence pairs in table \@ref(tab:senpair1) and complete the following activity with your partner.
| Initial Statement | Additional Information |
|---|---|
| Our method … Shared power sources, advanced cloud computing | avoids drawbacks of other methods (e.g. x and y). |
| Their study failed to take into account that levels of bureaucracy are not uniform throughout the same nation. | Their study only considered level of bureaucracy in the national health system, not in local or national government in general. |
| Metallurgists study metals, how they can be extracted, and what properties they hold. | Metallurgists investigate how the properties can be modified in order to produce allows. |
| Their conclusion regarding a lack of relationship between bureaucracy and complexity of language is erroneous because they only investigated two languages. | The two languages are very similar — France and Spain are neighbouring countries with very similar languages. |
```{exercise, name=“Emphasising contrasts”}
The following transition phrases and words emphasise contrast. Re-write the sentence pairs in table @ref(tab:addition) using one of the transitions in table @ref(tab:compare) to combine the information. You may have a single sentence with a transition word in the middle, or two sentences, with a transition word at the beginning of the second sentence.
| *Statement* | *Contrast* |
|------------------------------------|------------------------------------|
| Centipedes are hunters | Millipedes are herbivores. |
| Traditionally it was thought that men don't express their feelings or talk about their problems because they are repressed. | Men are able to talk about their personal problems but do not see the utility of doing so. |
| When water boils in an uncovered container, it produces about 2 000 times it's own volume of steam. | In a sealed container, steam cannot expand and pressure increases. |
| There is very strong evidence that the universe began around 13.7 billion years ago. | Some religious fundamentalists believe that the world was created on October 22, 4004 BC. |
: (#tab:addition) Using transitions to contrast information.
```{exercise, name="Balancing statements"}
Choose at least one of the following topics. Write at least one one advantage (pro) and disadvantage (con) pair for each of the topics and connect the phrases with a transition.
- Democracy
- Genetically modified organisms
- Vegetarianism
- Travelling abroad
- Studying history
- Plastic surgery
- Free trade agreements
- Electric cars
- Prenatal genetic testing
- Eco-tourism
Both order and transitions make your writing cohesive. We’ve already seen some examples of being consistent. In the next section we’ll go into a bit more depth.
22.4 Scientific Writing is Consistent
Although you want to have consistency in you naming conventions and parallel structures, try to vary non-critical word choice as much as possible to avoid dull writing. Generally, avoid using the same word twice in one sentence and, if possible, in adjacent sentences. Exceptions include cases when word repetition emphasizes key terms or when it creates parallel structures.
22.4.1 Use Grammatically Parallel Structures
Word repetition can be a powerful approach to reinforce understanding. You can repeat the same words or phrases in a sentence if this creates grammatically parallel structures. Parallel structures can be used by the writer to “drive a point home”. Without parallel structures, the reader often needs to do more work to understand a sentence.
Grammatically parallel structures use the same sentence structure to highlight informative comparisons. You can create a parallel structure by repeating either the subject, the verb or the completing phrase.
```{example, name=“Use Consistent Language to Create Continuity”}
In the first sentence , the writer attempted to vary word choice, using belong to and reside in. This variety of word choice comes at the cost of understanding. The reader briefly struggles with the fact that the parallel structure they expected is absent. Without this, the reader needs to know that reside in and belong to mean the same thing.
👎 Although there is agreement that humans and chimpanzees reside in the same taxonomic order, there is controversy regarding whether they belong to the same taxonomic family.
👍 Although there is agreement that humans and chimpanzees reside in the same taxonomic order, there is controversy regarding whether they reside in the same taxonomic family.
👎 Instead, the question is whether culture, learning, and language play a minor role in complex emotional responses (basic emotion theory) or a substantial one (constructionist theory).
👍 Instead, the question is whether culture, learning, and language play a minor role (basic emotion theory) or a major role (constructionist theory) in complex emotional responses.
👍 Instead, the question is whether the role of culture, learning, and language in complex emotional responses is small (basic emotion theory) or large (constructionist theory).
In the first paragraph, the differential response of the mutant lines is not clearly expressed. The “take-home” message from the comparison is not clear until it is stated at the end of the paragraph.
👎 Treatment with Reagent X inhibits filopodia extensions by down-regulating yfg1 in wild-type mice. In yfg1\(^{-/-}\) and yfg2\(^{-/-}\) mice, filopodia extensions are inhibited only after prolonged exposure to Reagent X. However, Reagent Y is needed in addition to Reagent X to inhibit filopodia extensions in yfg3\(^{-/-}\) and yfg4\(^{-/-}\) mice. These findings indicate that mutant backgrounds have different responses to Reagent X.
In the second, improved, paragraph a parallel sentence structure is used to make the comparison easier.
👍 Treatment with Reagent X inhibits filopodia extensions by down-regulating yfg1 in wild-type mice. However, mutant backgrounds have different responses: yfg1\(^{-/-}\) and yfg2\(^{-/-}\) _mice lack filopodia only} after prolonged exposure to Reagent X, yfg3\(^{-/-}\) and yfg2\(^{-/-}\) mice lack filopodia only in the presence of both Reagent X and Y.
### Assigning Several Topics to a Paragraph
If you need to include more than one topic in a paragraph, ensure that the topics can be connected under a unifying heading. If you can write a topic sentence that unites several ideas, then you have a single paragraph. If you can't, you don't.
The following three topics...
- *Cavefish lack functional eyes*
- *Cavefish have chemoreceptors on their body surface*
- *Cavefish have very efficient metabolism when swimming*
... can be presented as a single paragraph by unifying them under a single topic sentence:
- *Cavefish show many adaptations to life in the dark*
When discussing many topics in a paragraph, signal all topics and keep their order consistent. Introduce the new items at the start of the paragraph and present them in the same order within the paragraph. When going into detail about each topic, place the key- word at the beginning of the sentence. If the discussion is too long, divide topics into separate paragraphs and use transition sentences to link them together.
```{example, name="Consistent Order & Naming Conventions"}
👎 Changes between cellular states can be quantified by measuring relative protein abundance in the two samples. This was done using two complementary mass spectrometry-based techniques: _Label-free quantification_ and _isotope labelling_. _SILAC_ (stable isotope labelling with amino acids in cell culture) requires amino acids containing heavy non-radioactive isotopes to be incorporated into the proteins of one sample. The heavy (labelled) and light (unlabelled) cell lines can be mixed immediately following lysis, thus avoiding sample preparation artefacts, and analysed simultaneously with high-resolution mass spectrometry. The relative intensities of peptide peaks reflect the relative abundance of proteins. In contrast, alignment of separate mass spectrometry runs is required with _label-free quantification_. The relative intensities of the same peptide peak in different runs reflect the relative abundance of proteins.
👍 Changes between cellular states can be quantified by measuring relative protein abundance in the two samples. This was done using two complementary mass spectrometry-based techniques: _SILAC_ (stable isotope labelling with amino acids in cell culture) and _label-free quantification_. _SILAC_ requires amino acids containing heavy non-radioactive isotopes to be incorporated into the proteins of one sample. The heavy (labelled) and light (unlabelled) cell lines can be mixed immediately following lysis, thus avoiding sample preparation artefacts, and analysed simultaneously with high-resolution mass spectrometry. The relative intensities of peptide peaks reflect the relative abundance of proteins. In contrast, _label-free quantification_ involves the alignment of separate mass spectrometry runs. The relative intensities of the same peptide peak in different runs reflect the relative abundance of proteins.
There are two problems with the first paragraph.
1. The SILAC method is referred to using different names ("SILAC" and "isotope labelling").
2. The order of the signals ("Label-free quantification" and "isotope labelling") is not consistent with the discussion.```{example, name=“Consistency”}
👎 In addition to studying job demands that are present, burnout researchers have investigated a lack of job resources. The resource that has been studied most extensively has been social support, and there is now a consistent and strong body of evidence that a lack of social support is linked to burnout. Lack of support from supervisors is especially important, even more so than support from coworkers. Within the social support literature, there is also a “buffering” hypothesis that suggests that social support should moderate the relationship between job stressors and burnout (i.e. the relationship will be strong when social support is low, but weak when support is high). However, studies of this hypothesis have met with mixed success, and it is not clear whether this outcome is due to methodological or theoretical issues.
👍 Research in burnout has focused on both the presence of job demands and the absence of job resources. The resource that has been studied most extensively has been social support, and there is now a consistent and strong body of evidence linking burnout with a lack of social support. Lack of social support from supervisors is especially important, even more so than support from coworkers. Within the social support literature, there is also a “buffering” hypothesis that suggests that social support should moderate the relationship between job stressors and burnout (i.e. the relationship will be strong when social support is low, but weak when support is high). However, studies of this hypothesis have met with mixed success, and it is not clear whether this outcome is due to methodological or theoretical issues.
```{example, name="Consistency"}
👎 _Several themes_ emerged from these early interviews in the human services, suggesting that the burnout phenomenon had some identifiable regularities. _First,_ it was clear that the provision of service or care can be a very demanding and involving occupation and that emotional exhaustion is not an uncommon response to such job overload. _The second component_ of depersonalization (cynicism) also emerged from these interviews, as people described how they tried to cope with the emotional stresses of their work. Moderating one's compassion for clients by emotional distance from them ("detached concern") was viewed as a way of protecting oneself from intense emotional arousal that could interfere with functioning effectively on the job. _However,_ an imbalance of excessive detachment and little concern seemed to lead staff to respond to clients in negative, callous, and dehumanized ways.
👍 _Two themes_ emerged from early interviews with human resource departments. _First,_ being a care provider can be a demanding occupation. Emotional exhaustion is not an uncommon response to such job overload. _Second,_ depersonalization (i.e. cynicism) serves as a coping mechanism with the emotional stress. Moderating one's compassion for clients by emotional distance from them ("detached concern") was viewed as a way of protecting oneself from intense emotional arousal that could interfere with functioning effectively on the job. _Unfortunately,_ an imbalance of too much detachment and too little concern appears to lead staff to respond to clients in negative, callous, and dehumanized ways. These findings suggested that the burnout phenomenon had some identifiable regularities.
```{exercise, name=“Bringing it all together”}
Together with your partner, edit the following sentences implementing the principles of good scientific writing discussed so far.
This paper provides a review of the fundamental principles of conservation biology study design, citing as examples previous investigations that illustrate methodological challenges or that demonstrate successful solutions to the difficulties specific to conservation research..
These findings imply that the rates of oxygen radical production and recycling are equivalent among murine neonates but not equivalent during senescence, with the rate of oxygen radical production exceeding that of its recycling back to superoxide.
For example, cluster C4 shows strong H3K4me3 downstream of the TSS and H2A.Z enrichment both upstream and downstream of the TSS whereas cluster C6 has a similar H3K4me3 pattern, but H2A.Z shows higher enrichment upstream of the TSS.
```{exercise, name="Building paragraphs"}
Each group of statements below contains a problem, a consequence of this problem and a solution. Choose one group and build a short paragraph using the material covered thus far in the workshop. For each group identify what the topic of the paragraph is going to be. You can add sentences not present.
- Gap between poor and rich countries increases.
- Brain drain (top scientists leaving poorer country for richer country)
- Rich countries set up and fund labs in the poorer country, without 'stealing' that country's scientists.
- The poorer country loses its best scientists and thus revenue sources.
---
- Most presentations at international conferences are poorly presented, poorly structured and boring.
- The value of much research is lost.
- Courses on how to give interesting and effective presentations should be held in research institutes around the world.
---
- Diseases that affect huge areas of Africa are neglected.
- The majority of biomedical research is aimed at treating illnesses that are prevalent in the industrialised world.
- Priority should be given to the numbers of people affected by a disease, rather than the geographical location of the sufferers.