- 1 THE BIO-EDITOR: A WRITING GUIDE FOR KOREAN SCIENTISTS (바이오에디터)
- 2 Table of Contents
- 3 Introduction
- 4 The Format of Technical Papers
- 5 Spell-Check Please
- 6 Editing Marks and Notes
- 7 Editing Marks Key
- 8 Abbreviations
- 9 Writing Checklist
- 10 Writing Style
- 11 Use a Direct Writing Style
- 12 Use of the Active Voice
- 13 Clarity is Important
- 14 More on Exaggeration
- 15 Paragraph and Paper Unity
- 16 Transition Sentences
- 17 Grammar and Usage
- 18 Grammar
- 19 Articles
- 20 Plurals
- 21 Verb Tenses
- 22 Parallel Subject and Verb
- 23 Use the Infinitive
- 24 Avoid Verb Shifts
- 25 Usage
- 26 Use of “of”
- 27 Sentence Length
- 28 Relationships
- 29 Abbreviations
- 30 Use of “all”, “the whole”, and “entire”
- 31 Non-Count Nouns
- 32 Use of Capitals
- 33 Comparison
- 34 Use of “in time”
- 35 Quantifying Adjectives and Phrases
- 36 Use of Prepositions
- 37 Use of “such as”
- 38 Use of “and” and “also”
- 39 Use of “but”, “yet”, and “however”
- 40 Use of “on” and “in” and “at”
- 41 Use of “it” and “this”
- 42 Agency
- 43 Punctuation
THE BIO-EDITOR: A WRITING GUIDE FOR KOREAN SCIENTISTS (바이오에디터)
by Maryana Bhak
with Jong Bhak
Please reproduce any or all of this guide freely and share it with anyone who could benefit from its advice. We ask only that you reference the work when doing so.
Purposes of this Guide
This guide is specifically for Korean-speaking science writers to address common challenges you may have. It has three purposes:
- to give you a checklist to prevent or catch errors before I actually edit your papers,
- to explain my editing marks and notes, and
- to go into more discussion about writing papers in English, in terms of style, grammar and usage, and punctuation.
Another result of reading and using this guide is that your oral presentations in English may become stronger.
My Role as Editor
It is my pleasure to offer my native knowledge of English and my experience writing and editing to you in hopes that your scientific manuscripts will be published. I am highly and humbly aware that your English will always surpass my use of Korean and would like to acknowledge that before I begin respectfully to correct your excellent English writing. Also, I realize that I am privileged to speak the default common language of the world and am not proud of the reasons why it is so (but that is another book). Know that I do not take this privilege for granted, and that I offer my help in the spirit of sharing good science and of the continued success of Korean scientists in its pursuit.
My background is in intercultural communications, conflict resolution, and adult education practice and administration, primarily English as a Second Language with Asian students. If my lack of scientific education makes you nervous, know that I have edited papers that have been published in, for example, Nature Genetics, Science, Bioinformatics Journal, Journal of Molecular Biology, BMC Bioinformatics, Genomics & Informatics, and Genome Informatics Journal, and have written successful grant proposals on the order of hundreds of thousands of dollars from government and corporate funders.
Because I do not have a formal background in science, in my role as an English editor I am looking only at grammar usage, punctuation, and writing style. I may not understand the idea in a sentence, but I can tell if the grammar is wrong or the word order is confusing. Your supervisor or senior writer should be responsible for the scientific aspects of your paper such as overall coherency and scientific validity, consistency of theme and conclusions, and specific meaning of sentences. This includes your use of abbreviations and scientific terms used in your paper. For example, if you have abbreviations in the abstract without the full words, I will assume that everyone knows what they mean.
There are many books out about proper grammar, punctuation, and writing style. I tend to follow the traditional, stricter rules, and American spelling and usage (Strunk and White’s Elements of Style is my favorite)—although I am also very familiar with British English. Your English teachers or books you have read may have different opinions on certain rules, especially about commas and hyphens, long, complex sentences versus short, concise sentences, and other ongoing word wars. My advice on this issue is this: “At least be consistent. If you want to use a comma where I would not recommend it, always use it in that way. Do not go back and forth, not only because it looks sloppy, but because it can confuse the reader.”
My overall goal is to never have the reader think about your writing style; we want her/him to think only about how important and interesting your work is. Since most of your peer reviewers will be western, I also offer some understanding of culturally-based differences in writing styles that may help to make your papers stronger.
One of the best ways to improve your writing and understanding of English grammar and style is to read English writing as much as possible. Read a journal article about something you are very knowledgeable with an eye to the writing style instead of the topic. Read it several times, thinking about the Editing Checklist items on content such as “I can say in one sentence what this paper is about.” Read English language newspapers and short stories or novels for further exposure to the flow of ideas and expression. Be an active reader, conscious of the content and style of the writing, as opposed to a passive reader, merely trying to understand the meaning of the words and sentences for entertainment or learning: try to see the different ways of expressing ideas or feelings. How did the author communicate effectively to you?
The Format of Technical Papers
I will assume you are following the format required by the journal to which you will submit your paper. If something is glaringly missing or mis-ordered, I will make note of that, but otherwise take no responsibility if your paper is rejected because of formatting problems.
Refer to journals’ websites for concise requirements for formatting and editing, e.g., www.biomedcentral.com/bmcbioinformatics/ifora/#defaulttype for BMC Bioinformatics, which not only includes detailed instructions, but also resources and other links.
There are many words that come up in Word as being spelled incorrectly in your paper (they have a red, squiggly line under them), simply because you are using many scientific and technical terms not commonly used. Still, you may have spelling errors of common words and should correct them before giving it to an editor.
Editing Marks and Notes
I may not know the vocabulary or common use of certain phrases, so disregard any marks on words or phrases that are actually correct and acceptable in the field. Also, I may misread something, especially if the sentence is long, so again disregard my marks.
There are instances when I do not know if something is singular or plural, but it is certain that you need to either use an article or make it plural, because the grammar is wrong. Double check those corrections. (This comes up frequently, as it is the most common area of error for you.)
Example: “…proteins which were located in cytoplasm or nucleus…” is incorrect, but could be either “…proteins which were located in the cytoplasm or nucleus…” (if they are singular) or “…proteins which were located in cytoplasm or nuclei…” (if they are plural — cytoplasm is non-count, so it does not change).
Example: “…of a soluble protein is the presence of signal peptide in its N-terminus…” is incorrect, but could be either “…of a soluble protein is the presence of a signal peptide in its N-terminus…” (if it is singular) or “…of a soluble protein is the presence of signal peptides in its N-terminus…” (if it is plural).
In either of the above cases, you need to make a change in the grammar, but you have to decide. I will put both choices with an underlined “or” to show I do not know which one is appropriate.
Note that in my handwritten notes to you, I do not always use full grammar or proper spelling (for example, I leave out “I” and articles and use “thru” instead of “through”). So do not use my notes as examples of good writing! If I make a mark with “OK” over it, that means disregard the mark—I changed my mind or realized it was not incorrect.
If I am not sure about the usage or proper word choice, I put a question mark at the end of the line or above the word, sometimes with a suggestion or two. You should decide which to use or ask your supervisor to advise you.
If I use quotation marks, they indicate what words to put in, not that you should include the quotations marks. They are simply to distinguish my notes from my suggested correction.
The following page is a key for the editing marks I use; most of them are common symbols for editing.
Editing Marks Key
- sp = spelling error
- sing = singular
- pl = plural
- n = noun
- v = verb
- adj = adjective
- adv = adverb
- SVO = Subject-Verb-Object
- vt = verb tense shift
Before you give a paper to me, please check it yourself.
___ I have used the proper format for the journal to which it will be submitted, including sections, headers and sub-headers, paragraph tabbing, line spacing, references, etc.
___ Any terms abbreviated in the abstract without explanation are commonly known in the field.
___ I can say in one sentence what this paper is about.
___ My paper and paragraphs clearly have unity—the whole paper has one overall idea (unless explicitly stated otherwise), each paragraph has one idea relating to the whole paper.
___ The main or most important idea of each paragraph is explicit in the first sentence of that paragraph.
___ My abstract, introduction, and conclusions have unity (the reader can say in one sentence what this paper is about).
___ I have deleted all irrelevant or redundant information or findings.
___ I am clear and direct, and I avoided vague, ambiguous or exaggerated terms, even if my data or methods are not perfect or strong.
Grammar and Usage:
___ I have read the paper aloud to self-edit grammar and usage errors.
___ I have double-checked plurals and singulars and added s/es when needed.
___ I have double-checked my use of articles and added a/the when needed.
___ I have checked “between” and “among” usage.
___ I have done a spell-check to correct common word spelling.
___ I have double-checked my use of the word “of” and made some nouns into adjectives or added possessive pronouns.
___ I have checked my verb usage to be sure I am consistent and logical with present and past tenses, and there is subject/verb agreement.
Everyone has a different way to write papers. Some make a detailed outline first and fill in the text later, some just write down as much as possible and organize the text later, and others do a combination of each. Some of you may write in Korean and then translate into English, and others write directly in English. I would recommend that you write in English, as it will save time, and you will be less likely to have syntax or word order problems—perhaps with a phrase or sentence in Korean to translate later with your supervisor or group members. If you cannot do so, you should take some higher level technical writing and English grammar classes. Also, you may be writing as a team with different parts being written by different members. As long as you get a good final product, it does not matter how you got it. If you find your papers are never quite working out, you may want to try a different technique. Perhaps when you write in English, you need to be more intentional in making an outline, even if you usually do not do so.
What is important is that you end up with a paper that is cohesive, i.e., its parts work together to show your intent, and coherent, i.e., it sounds good and makes sense to the reader. Keep your reader in mind, especially as you work on final drafts of your paper. Ask yourself if you have communicated what you want the reader to receive without having to read between the lines or getting lost in a tangle of ideas and too much detail.
Here are some basic rules of thumb to follow when writing for a primarily western audience.
Use a Direct Writing Style
Most western readers do not like to “read between the lines”, i.e., guess at indirect or “soft” communication. Be sure to say what you want to say and not assume the reader will look into your text to find the point of the paper or paragraph. Even if s/he can extrapolate from inferences or indirect expression, it is bothersome to have to do so, and may leave the reader unsure of your grasp of the material. Ask yourself, “What, in one sentence, is the point of this paper? Of this paragraph? Will my reader also find that point explicitly stated?”
Along with being explicit about your purpose, your methods, and your findings, it is important to leave out any extraneous information. Keep sentences tight, simple, and clear. If a sentence is getting too long, break it into two or three shorter ones. Do not repeat information or ideas in the hopes of the reader believing you more; in fact, like using vague language to cover up weakness in the work, it will highlight the possibility that there is a problem with your data, methods or findings.
Use of the Active Voice
Along the lines of being direct is using the active voice (preferred by professional journals). Generally, the passive voice is not as strong or straightforward, again potentially bothering the more direct, assertive style of western writers/readers. The passive voice leaves the agent of the action unknown or unclear, whereas the active voice leaves no question as to who is doing the action.
Example: “The prediction accuracy of iPSORT for signal peptides was also investigated.” --> “We also investigated the prediction accuracy of iPSORT.”
Example: “It has been discovered that many AREs are present in the poly-T regions.” --> “Kim and Smith discovered that many AREs are present in the poly-T regions.”
Clarity is Important
Avoid vague words and phrases such as “around”, “a few”, “about”, “many”, and “less than 80%”. They make the reader be bothered by questions like, “How many is ‘many’—50 or 5,000?”, “How much less than 80%—79% or 72%?”. Be specific and accurate.
Example: “…found that around half of the longest AREs were derived…” State instead that “…48% were derived…” or “…between 45% and 51% were derived…”.
Write what you found. Be direct and clear. If an aspect of your findings was weak, using vague terms will make it seem even weaker, because it brings attention to your wanting to avoid being specific. Exaggerating findings with vague terms or misinformation can also make your ideas seem weak, since there is a good likelihood that the reader will suspect you are not being accurate. If there was a problem or finding that did not support your hypothesis or proposal, state that and explain why it does not take away from the general findings of your work. Or consider having a different theme for your paper, showing that you went into the research with something in mind only to find that it did not work that way, because… (whatever you found instead).
More on Exaggeration
You should remain factual and objective when writing about scientific work. Again, using exaggeration, emotive words, or too much emphasis with strong adjectives can draw the reader away from your ideas to thinking about your motives.
Some of the problem here may simply be word choice: some words are better used in informal writing and some in technical writing.
Example: “…the hub families have an extremely high number of interaction partners…” --> “…the hub families have a significantly high number of interaction partners…”
On the other hand, you may be choosing what are called “persuader words” which, as their name suggests, are used in an attempt to persuade the reader that what you are writing about is true or important. Because use of words such as “obviously”, “surely”, and “clearly” can trigger the reader to ask, “Well, is it obvious?”, it is better to leave them out and instead state your premise with supporting data or evidence.
Example: “One obvious outcome of the interactome comparison was the presence of…” --> “One outcome of the interactome comparison was the presence of…” (If your data is accurate, it will support your statement.)
Paragraph and Paper Unity
At times when you are trying to get all your ideas and information into writing, the forest gets lost for the trees. The question to ask when going over your draft is “Is there unity in my paper?” If you get feedback from your supervisor or editor that there is too much information or your paper gets repetitive or it is not clear what your point is, or if you are unsure if you have “said what you want to say”, ask this question. Go through each paragraph and then think about the whole paper asking the question, "Is there unity?".
Each paragraph should be basically about one thing, for example, one step in the methodology. If there are sentences or details in the information that do not go with the paragraph, put them somewhere else—in another paragraph or in another paper.
Begin the paragraph with a strong sentence telling what you are going to show in it (with the exception of the introduction in which your last sentence should be something like “in this article we will…”). End the paragraph either with the last bit of information on the paragraph’s topic or with a transition to the next paragraph. This may feel unnatural for you, and you may find yourself wanting to write the strongest point in the last sentence. However, while s/he is not conscious of it, western readers will not see it as the important part, so it will not be as effective. This is not a matter of judgment, but a subtle worldview difference. (See more about “beaming out” in the Grammar and Usage section.)
Now, do the same with the paper as a whole. Do all the paragraphs belong with your main ideas? If not, put them in another paper. Is your abstract summarizing exactly what you say in your paper? Does your introduction explain what your intent was when going into the work and that you achieved it? Does your conclusion show that you managed to achieve your intent and that you found your expected results? Is there new information in the conclusion that is not in the introduction? Put it in the introduction or in another paper!
Although you want your paper to be as short and succinct as possible while including all relevant information, you also want to have a smooth transition from one paragraph to the next, making it easy for the reader to see where you are going. Therefore, the use of transition sentences at the end of a paragraph is a helpful way to do so.
That last sentence in the above paragraph is (I hope) a good example of a transition sentence. It is a kind of indicator that I am moving on to another point in my discussion about the topic of transition sentences. Using words such as “therefore”, “although”, and “furthermore” shows the reader that you intend to extend your discussion in the next paragraph. There are basically two kinds of transition sentences.
That last sentence was the second kind of transition sentence (the first kind being one with an indicator word like “therefore”. It indicates what I will write about next—in this paragraph—i.e., about the two kinds of transition sentences. This second kind of transition sentence does not have a specific transition word, but the meaning shows that I will probably give the two examples of transition sentences. In your paper, you may use a transition sentence like this second type to show two steps in your methodology or two examples of how to benefit from using a new database.
Of course, you will not always need a transition sentence for each paragraph, especially if it is the last one in a section (the next subheader will indicate the next paragraph topic). However, if your editor or supervisor has given you feedback that s/he is not clear on the direction of the paper or that it is not organized in a logical way, working on transition sentences will either 1) help the reader follow the direction you are going, or 2) help you to see that you need to reorder your paragraphs or eliminate a paragraph that belongs in another paper because it does not directly pertain to the paper topic. In other words, they can be tools for improving your writing style.
Grammar and Usage
At the heart of communication are grammar and usage. Unfortunately, as you have learned in English classes and trying to talk with westerners and understand their ideas, we have very different ways of communicating. Language can show us a lot about cultural differences, the ways we develop our values and behaviors, and how we think and transmit our thinking. Simply by trying to communicate with and understand Korean and Chinese people, my speaking and writing style has changed. In the past, I would have begun this paragraph with “I” behave in such and such a way, because I am American-born. Now I use “we” a lot more and try to get at ideas from different perspectives. One of the most basic of these (not widely known or understood) is the deductive or “beaming out” tendency of westerners and the inductive or “beaming in” tendency of Asians. It shows up in our grammar and in how we view the world and our place in it. (For an excellent explanation of this cultural aspect of communication, watch EBS's documentary: East and West: https://www.youtube.com/watch?v=RnyaD1ZjS-s )
Most of your readers will not have had that in-person experience and will not be able to say, “Oh, s/he is trying to say such and such but uses a different syntax because s/he is Korean.” Therefore, your submitted paper must be grammatically correct, not just in general, but specifically in more subtle ways such as word order and phrase order, as well as sentence placement.
A note on all the “exceptions to the rule” in English. Often when something does not seem to follow a rule or is an exception to the rule, there does not seem to be a good reason why it is the case. This is the most difficult part of learning to be fluent in a language. Usually, the exception is because of an idiomatic usage or an evolution in the language that is not necessarily logical. The answer to the question “why?” is “because that’s the way we say it”. If you are interested in etymology, you can spend a lot of time looking up these exceptions; otherwise, become as familiar as possible with them, by reading English-language books and watching shows or talking with native speakers.
As you know, most English sentences are based on SVO (Subject-Verb-Object) syntax, instead of the Korean SOV syntax. What happens when your sentence is more complex? To check if the grammar is correct, parse the sentence to find the fundamental parts: subject, verb, and object (if any). Make sure they agree, and think about the order of phrases—do they work with main idea first and add on phrases to a later or the last part of the sentence? Or could they be unclear as to what they are referring, thus potentially confusing the reader? Or do they clue the reader in to the fact that you are not a native English speaker?
The most common errors in your writing are 1) leaving out articles, 2) not adding “s/es” to make plural words, and 3) being inconsistent with your verb tenses.
You know these rules, but it is where you all make the most errors in your papers (along with not making plurals plural), and it is the sure way your reader will know you are not a native-English speaker. Maybe reading aloud can help you notice where the articles are missing.
A short review: Generally, you always need an article before a singular noun and sometimes before a plural noun. “a” means one of many or in general or the initial time something is mentioned. “The” means the only one, the specific one or the one mentioned already (often with “a”). There are lots of exceptions.
Example: “…to analyze interactome level interaction information using relatively complete set of distinct protein structural families.” --> “…using a relatively complete set…”
Example: “Due to large size difference, it will…” --> “Due to the large size difference, it will…”
Now for a long review, please go to one of your old English textbooks and do all the exercises about articles.
Again, you know the rules, so read aloud to hear where “s/es” is missing. Also, be careful with non-count nouns such as “information”, “homework”, and many concept words: they often do not get an “s/es”.
Example: “Our results corroborate previous studies on well-conserved and minimal gene set.” “Our results corroborate previous studies on well-conserved and minimal gene sets.”
On the other hand, some words are usually plural in technical writing, such as “results”, even though that may seem strange.
Example: “From the result of phylogenetic profile analysis…” “From the results of phylogenetic profile analysis…” (You may have only conducted one analysis of something, but you always use “results” when writing about that analysis, as in both examples!)
Other words usually plural in technical writing are: remarks, acknowledgements, and references.
Be careful with Latin-based words, since often they do not follow the s/es rule. For example, “nucleus” is singular and “nuclei” is plural; “criterion” is singular and “criteria” is plural.
Use the simple present tense when something is generally true, a fact or a habit.
Example (true): “PSIbase is the first protein structure interaction database.”
Example (fact): “Cells have several organelles.”
Example (habit): “We use PSIBLAST to determine the homology among sequences.”
Use the simple past tense to show something done in the past that is finished.
Example: “We measured the intensity of sunlight and found more insects are active at higher temperatures.”
Example: “Past studies determined that proteins contain at least 20 amino acids.”
Generally, unless you are very comfortable with perfect tenses (e.g., “have shown”), keep to the simple, future, and continuous forms. If used incorrectly, use of the perfect tense can make a sentence at the best awkward and at the worst very unclear. The benefit of using the perfect tense is that it can give a subtle change in meaning that can make writing very clear.
Example: “Over 160 genomes were completely sequenced.”
The above sentence is true and correct grammatically. However, because it is leading into a discussion about what this information now allows scientists to do, a more accurate and specific way to say it would be, “Since 1999, over 160 genomes have been completely sequenced.”
Another place of potential misunderstanding is in the use of modals, so again, unless you are sure of their use, stick to simpler ways of getting your ideas across. Especially problematic seems to be the use of “could” which can be a modal or the past tense of “can”. To avoid confusion, use the past tense of the main verb, or use “to be able to” (was able to), instead of “could”, unless you mean something is possible (“could be” or better “may be able to be”) under certain circumstances. (The difference between “성공적으로 가능했다” and “그런것이 일반적으로 가능할 수도 있다”.)
Example: “This computational, evolutionary, and structural analysis could show an extensive comparison of genome interaction networks within a homogeneous paradigm.”
The above example seems to mean that the study was done and the analysis showed a comparison (simple past tense). However, the use of “could” makes it ambiguous. The sentence could also mean that it is possible that a comparison would be the result, but not necessarily (modal). To avoid ambiguity, either say, “This…analysis showed…” or “This analysis may be able to show…”, depending on the intended meaning.
Example: “…species distinction could be analyzed by the comparison of interaction network architectures.” Does this mean we are now able to analyze the distinction? Then use the simple present “can be analyzed”. Or that it was possible to analyze? Then use the simple past of “can” (“was able to be analyzed”). Or that someday it may be possible to be analyzed? Then it is alright to use the modal “could be analyzed”. Or that someday it will be possible to be analyzed? Then use “will be able to be analyzed”. You see how many ways there are to interpret what seemed at first to be a fairly simple sentence!
Parallel Subject and Verb
Be especially careful when you use a singular subject and then a phrase with a plural noun and then the verb, or when you use a plural subject with a phrase with a singular noun followed by the verb.
Example: “…an increasing number of observations have been made on unstable species…” is incorrect, because “…number has been made…”.
Example: “The key advantages of the PDB-derived predictive bioinformatics method is that…” is incorrect, because “…advantages are…”.
Example: “…A significant portion of mammalian mRNA sequences contains AU (Adenine and Uracil) rich elements…” is perfect, even though it may sound strange, because “…portion contains…”.
With the phrase “There is/are…”, look to the object to decide whether to use first or third person for your verb.
Example: “…as there are a great number of multi-domain proteins.” is incorrect, because “there is a great number…”.
Use the Infinitive
When using a secondary verb within a sentence, do not use ‘for -ing’. While it is grammatically correct, it is not common usage, and therefore sounds awkward.
Example: “We used three concepts for constructing equations for estimating the ages of species and a species-homology measurement for 153 completely sequenced genomes.” “We used three concepts to construct equations to estimate the ages of species and a species-homology measurement for 153 completely sequenced genomes.”
Avoid Verb Shifts
Generally, stick to one verb tense (past or present usually, with the various perfect and modal tenses as well). Check if all the verbs in each sentence and paragraph are in the present or past tense. Of course, if you are using the present for the most part but are mentioning, for example, a finding of the past, you will switch to the past tense—just make sure you then return to the present tense for the rest of the sentence or paragraph. This self-editing is difficult, but very important, since it can make the reader feel something is strange about the tenses or give the wrong information or meaning.
Example: “SWISS-PROT contains 1450 kinds of the subcellular localization descriptions in its “CC” field. The localo-orientations of proteins were defined using these descriptions. There were 628 kinds of descriptions indicating ‘in’ (7325 proteins) and 194 ‘out’ (2042 proteins) localo-orientations. Approximately 42% (1870) of eukaryotic PfamA domains inherited localo-orientations from proteins to which they belong. These domains contained 1436 ‘in’ and 434 ‘out’ domains.”
Notice that both past and present verb tenses were used. This is clearly correct, because the first sentence is showing a general fact of SWISS-PORT data (it still contains 1450 kinds), so the present tense should be used. The rest of the paragraph is about the research that was conducted, that is finished (with the exception of “proteins to which they belong”, because they still belong—it is a fact), so the past tense should be used.
Another correct example:
“Considering these additional TM helix containing domains, 12% of domains had at least one TM helix. A relatively high amount of domains for the TM helix number of seven is possibly due to the biased active research for rhodopsin-like receptors.”
Notice that the second sentence is in the present tense. That is because it is a comment about the possible reason why there was a high amount of domains; the possibility is still true.
Example (of unclear verb tense shift):
“Using the defined information of domains in Step 1.1 as a standard, the localo-orientations of the remaining domains were assigned in multi-domain proteins in consideration of the domain relationship. Domains in soluble proteins inherit the localo-orientations of coexisting standard domains. In transmembrane proteins, localo-orientations of loops among TM helices were alternatively assigned. If proteins have signal peptides and no standard domain, the N-termini of these proteins were assigned to be ‘out’.”
Notice that both past and present tense were used. That is acceptable, as long as the meaning is accurate and the author intended the shift. However, I checked directly with one of the authors and in fact, the past tense was intended throughout. So the paragraph reads more accurately as:
“Using the defined information of domains in Step 1.1 as a standard, the localo-orientations of the remaining domains were assigned in multi-domain proteins, considering the domain relationship. Domains in soluble proteins inherited the localo-orientations of coexisting standard domains. In transmembrane proteins, localo-orientations of loops among TM helices were alternatively assigned. If proteins had signal peptides and no standard domain, the N-termini of these proteins were assigned to be ‘out’.”
You can write a perfectly correct sentence in terms of grammar and punctuation, but still miss a subtler transfer of meaning. There are many examples of usage which differ in Korean and English, as well as habits or errors that you may make because you are writing about complex concepts in a language that is foreign to you, no matter how fluent you are. While they may seem like small differences to you, many readers will question your meaning and, unfortunately, your authority (“bad company fallacy” in logic, i.e., thinking that since your English writing has errors, your ideas may be weak as well). S/He will likely be bothered by an unclear sentence, for example, when you write “between” when you are talking about a relationship with several things and need to use “among”.
You probably learned these rules years ago in English class. Look at this as a review and to use as an explanation of why I correct these kinds of errors. If you find, paper after paper, the same problems, you may want to find an old exercise book and practice sentences with these usages in them or ask for a tutorial.
The following are the most common usage challenges I have found in papers written by Korean-speakers. You may not make all these errors, but should be aware of them as you read through your drafts and try to correct as many as possible before giving a paper to your supervisor or an editor. Also, try to understand and remember the corrections, so you learn and avoid making the same errors in future papers.
Use of “of”
In Korean, the possessive is expressed in the suffix “ui” (의), but in English, we use “of” as well as other means to show possessive such as adding “ ’s ” or a possessive pronoun, or using a noun as an adjective or descriptor.
To use “of” when a word or phrase can be used as a possessive or adjective is awkward in English writing, especially when used often. Therefore, use “of” sparingly and especially avoid using it more than once in a sentence. (Go back and read a longer text section of this guide and note how few “of’s” are used. For example, I write “SVO syntax”, not “syntax of SVO”.)
Instead of using “of” more than twice in one sentence, see if you can use a noun as an adjective.
Example: “This paper presents a hypothesis and evidence that Alu was one of the sources of the generation or origin of AREs.” “This paper presents a hypothesis and evidence that Alu was one source of AREs’ generation or origin.”
Example: “…structures of proteins of yeast and human…” “…structures of yeast and human proteins…” Or better yet: “…yeast and human protein structures…”
Or use a possessive noun or pronoun instead.
Example: “…that contains a poly-adenine region at the end of it…” “…that contains a poly-adenine region at its end…”
You are writing about complex ideas and processes, so it is natural for you to use long, complex and compound sentences. However, because of the word order and prefix/suffix problems, it may be better sometimes to write two or even three shorter sentences than a long one where the central meaning gets tangled up with additional phrases. Again, with the goal of not having your reader confused, you want to communicate your point clearly. Instead of forcing the reader to untangle a sentence, try to do that work yourself or with your supervisor. Of course, there needs to be a balance between having shorter, simpler sentences and too many short sentences that look like grammar school writing.
In Korean, “between” and “among” are the same word (사이). In English, however, it is important to distinguish between them (not “among them”, as there are only two words!).
The preposition “between” shows the relationship with two things.
Example: “The feelings between my father and me are strong.”
The preposition “among” shows there are relationships with three or more things.
Example: “The feelings among all my family members are strong.”
Make sure you are using these Latin abbreviations correctly.
“e.g.,” (exempli gratia) means “for example,”.
Example: “The contents of the box, e.g., the books and computer stuff, were lost in the move.” (there was other stuff, but it is not mentioned)
“i.e.,” (id est) means “that is,”.
Example: “The contents of the box, i.e., the books, computer parts, office supplies, binders, and disks, were lost in the move.” (there is nothing else in the box besides what is listed)
Note that “i.e.,” can also just point to explicitly what is meant.
Example: “Most Western readers, i.e., your journal editors, want to know precisely what you’re going to talk about in your paper.”
“et al.” (et alii ) means “and others”. Because “et” is not abbreviated, do not put a period after it.
“etc.” (et cetera) means “and the rest, and so on”. Do not use “etc.” in technical or formal writing, because it is too vague and open-ended.
Use of “all”, “the whole”, and “entire”
The direct translation of “all” into Korean is “the whole” or “the entire” (전체). Here is how to distinguish among them in English:
Use “all” with plural nouns.
Example: “…all the domains in yeast proteome were found to be…”
Use “the whole” followed by a singular noun, never plural.
Example: “…the whole structure has been found to be stable…” (and do not forget “the”!)
Use “entire” when the noun is singular or plural and you are referring to something being intact, as opposed to talking about inclusion (where you would use “all”).
Example: “It allowed us to predict protein structural interaction of entire genomes that did not have experimental protein interaction data.”
Many nouns represent something with too big a number (rice) or abstract (life) or amorphous (oil) to count. Although they can sometimes be made plural, usually they are not. Furthermore, they often do not require an article. Making them plural is incorrect; having an article is often correct grammatically, but it either changes the meaning or could sound strange to a native English-speaker and is therefore better without the article.
Example: “I ate the rice.” (meaning the specific rice that was on the table that day) or “I ate rice.” (meaning in general or as a habit)
Another common error (even among native English-speakers) concerning count and non-count words is the use of “less” and “fewer”. Use “less” with non-count and “fewer” with count nouns.
Example: “…although their interaction pairs were less than 1000.” “…although their interaction pairs were fewer than 1000.”
Use of Capitals
Sometimes you use capital letters for words that should not be capitalized or you sometimes capitalize a word, but then do not do so later in your paper. If your reader is asking, “Hmm, I wonder if there is a reason why this word is capitalized here but not there…”, s/he is not focusing on the ideas of your paper so much as your writing. This happens within sentences, in section headers, and in figures and tables.
Example: For section headers, use capitals consistently—
“Describing and comparing networks for the 147 species” and later “Core protein-interactome and peripheral interaction nodes of life”
“Describing and Comparing Networks for the 147 Species” and later “Core Protein-Interactome and Peripheral Interaction Nodes of Life”
Do not use capitals simply because a word is important; only do so if it is a proper noun such as “Markov model”, or is commonly capitalized in the field such as “Family”. If you are introducing a new term or using it in a new way, and you would like it to be capitalized, be consistent.
Example: “We termed this procedure the ‘Grammar Correction method’.” (Thereafter, it is always capitalized, but not in quotes as the reader has now been introduced to the term.)
When making a comparison, both or all items being compared must be explicitly identified, not implied, as in Korean usage.
Example: “In total, 1097 kinds of LocaloDom were used in the above two data sets. We checked the definition accuracy of these domains by comparing with the SWISS-PROT descriptions of corresponding proteins.” --> “In total, 1097 kinds of LocaloDom were used in the above two data sets. We checked the definition accuracy of these domains by comparing them with the SWISS-PROT descriptions of corresponding proteins.”
Example: “By comparing with the experimentally defined localization data, we showed our method can accurately predict the orientations of yeast proteome.” --> “By comparing the two samples with the experimentally defined localization data, we showed our method can accurately predict the orientations of yeast proteome.”
Use of “in time”
The idiom “in time” is used to show the timeliness of an occurrence (meaning soon enough).
Example: “We arrived at class in time to hear the whole lecture.”
“In time” is used with “just” for emphasis to show that it was almost too late.
Example: “I was just in time to catch the last train home. It left the station as I jumped on.”
To show the passage of time and its effect on a finding, use “over time”.
Example: "...As abstract information objects, cars evolved as much as human hair evolved over time. Hair is a product of hair cells while cars are the product of human brain cells."
Quantifying Adjectives and Phrases
For the most part, use exact numbers or amounts with either count or non-count nouns in technical writing, as discussed above in the writing style section. If, however, you are making a generalization about the field or a collection of work, you may want to use a quantifying adjective or a phrase to show approximate amount.
Use “much” with non-count nouns.
Example: “Not much information has been gleaned over the past several years about …”
Use “many” with count nouns.
Example: “These results have been low in many previous studies.”
Never use “a lot of” in technical papers. It is too informal. Use “a great deal” or “a significant amount” instead.
Example: “A great deal of sequences can be used to annotate proteins.”
Example: “The results of many BLAST searches have produced a significant number of errors in sequence alignments.”
Use of Prepositions
There are many subtle differences in the use of prepositions in English, but you can usually answer the question “why?” in these cases. Any grammar book will give you a good review of their use. Prepositions you have consistent trouble with are the following:
at/in Example: “in level” --> “at level”
Example: “…a domain-overlap can occur on the same protein sequence.” --> “…in the same protein sequence.”
Example: “…yet in a large scale.” --> “…yet on a large scale.”
Example: “…comparative interactome analysis for 147 genomes…” --> “…comparative interactome analysis of 147 genomes…”
Use of “such as”
If you break up a sentence with examples, use commas.
Example: “Experimental methods, such as microscopy for proteins tagged with a green fluorescent protein, have been available…”
If you use “such as” at the end of a sentence, do not use a comma.
Example: “…comparable result of the LocaloDom and the Grammar Correction method can be applied to accurately predict the localo-orientations in a proteome scale and can complement the experimental results such as low resolution microscopy.”
Use of “and” and “also”
“and” and “also” mean virtually the same thing, so you usually do not need both in the same sentence.
Example: “And the keyword fields were also used.” should simply be “The keyword fields were also used.” or “And the keyword fields were used.” (although using “and” at the beginning of a sentence is not the best idea in formal writing).
Use of “but”, “yet”, and “however”
“Yet” is most commonly used as an adverb indicating time, as in “something has not happened yet” (and is expected to happen sometime in the future).
Example: “We favor the expression data generated from various stimuli and the over-expression data measured in steady states (not available yet on a large scale).”
“Yet” is also a conjunction showing contrast or dissimilarity; however, “but” and “however”, more formal terms, are more commonly used to show this.
Example: “…the prediction results for all six targets coincided with known facts, yet the first two predictions were not reliable, due to their neutral regulatory patterns.” --> “… the prediction results for all six targets coincided with known facts, but the first two predictions were not reliable, due to their neutral regulatory patterns.”
(It gets more complicated than this in terms of parts of speech and usage; however, for the purposes of stronger writing, pay attention to the above examples for word choice.)
Use of “on” and “in” and “at”
“on a scale” “at” a level
we constructed a web-based comparative analysis tool, BioCovi, to visualize the homology information of mammalian sequences on a very large scale
The gene resides on the chromosome four at 103,779,572 location in human and on the chromosome three at 136,131,339 location in mouse.
Use of “it” and “this”
Use “it” the first time you mention something already named and “this” thereafter. Also, even if you have not used “it” in the first mention of something, still use “this” once the idea has been introduced.
Example: “It was reported to be of a power-law form… Overall, it indicated that the protein family interactome is scale-free.” “It was reported to be of a power-law form… Overall, this indicated that the protein family interactome is scale-free.”
Example: “Yeast has a greater number of hub families, and the hubs are larger… It can be viewed as an optimization of information processing…” “Yeast has a greater number of hub families, and the hubs are larger… This can be viewed as an optimization of information processing…”
Inanimate objects cannot influence other things without the direction or impetus of a person. For example, a database or computer program cannot determine relationships or find results without being designed or written by someone. You, a human being, can determine a relationship among data by looking at the information that is in the database. You can find results through putting some data into a program and seeing what comes out with the algorithms or formuli you wrote and instructed the computer to compute.
This is the problem of agency that sometimes shows up in your writing. Make sure you do not attribute work to some thing instead of showing it as the tool or vehicle that allowed you to do the work.
“Based on the comparative analysis of protein family interaction networks constructed by PSIMAP…”
“Based on the results of a comparative analysis of protein family interaction networks constructed by PSIMAP…” because PSIMAP cannot construct something without agency from a person.
While punctuation is similar in Korean and English, there are aspects of its use that should be noted and checked. For example, commas are used more frequently in English, and the rules can be complicated. Also, it is important to have correct spacing between words and punctuation marks. This also may seem unimportant—a little dot or dash—but to your readers, lots of little errors can be distracting and take away from the content of the paper; it can also be misleading or confusing if the lack or misuse of punctuation marks leads to a wrong idea.
Use a comma in a compound sentence that has two (or more) subjects, but not in a compound sentence that does not.
Example: “Genes required for each of these steps have been identified in yeast and were conserved among eukaryotes.” (no comma is needed, because there is only one subject)
“J class is the oldest one, S class is intermediate, and Y class is the youngest.” (commas are needed, because there are three subjects)
Generally, use commas around phrases, unless the sentence is very short.
Example: “Depending on the number of nodes and the interaction degree, the density of the graph varies, representing the complexity of the interatomes.”
In lists, use a comma between each item. (Some writers do not use one between the last two items, but this can be confusing, especially in longer sentences.)
Example: “…interaction networks among protein families is determined by 1) the number of nodes, 2) the number of interaction edges and 3) the architecture of the interaction link patterns.” “…interaction networks among protein families is determined by 1) the number of nodes, 2) the number of interaction edges, and 3) the architecture of the interaction link patterns.”
Example: “SBF and MBF are known to have some independent roles in budding, membrane and cell wall biosynthesis (SBF) and DNA replication and repair (MBF), respectively.” “SBF and MBF are known to have some independent roles in budding, membrane and cell wall biosynthesis (SBF), and DNA replication and repair (MBF), respectively.”
If there are commas within the items, use a semicolon between items, and/or use bullets, to avoid any confusion by the reader.
Example: “…three examples…are discussed: (1) the potential roles of eight chromosome 21 proteins in RNA processing pathways; (2) the chromosome 21 protein intersectin 1 and its domain composition, alternative splicing, protein interactions and functions; and (3) the interactions of ten chromosome 21 proteins with components of the mitogen-activated protein kinase…”
Colons vs Semicolons
Use a colon to show examples of the first part of the sentence (as I have done throughout this guide with my examples) or items in a list. A colon says, “Look.” The exception to this rule is in paper or book titles where you use a colon as a semicolon.
Example: “…we considered family members that belong to the following SCOP Superfamlies: a) multi-domain proteins, b) membrane and cell surface proteins and peptides, c) small proteins…”
Use a semicolon to add supporting or additional information that you would like to have so closely tied to the sentence that you keep it as part of the sentence (and in lists with commas, as mentioned above). A semicolon says, “Here’s more about that.” Usually you do not need to use “and” or “but”, but you may want to use a transition word such as “therefore” or “however”. The second part can also be a kind of repetition of the first part, but not an example.
Example: “…a set of atoms from a protein without any sequence order or 3D structure is not biological; it is merely physical and chemical.”
Example: “…gene expression data alone are often insufficient to detect the involvement of multiple regulatory inputs to target genes; therefore, this requires more detailed prior information.”
If you are using a two-word adjective, such as “two-word”, you often need a hyphen between the words, especially when you have a long string of adjectives.
Example: “…usually their well-established interactions…”
Example: “…the immune process of highly-evolved eukarya.”
Spaces Between Words and Punctuation Marks
Generally, there should not be any spaces between words and punctuation marks within a sentence, except for commas and semicolons. Sometimes in tables or figures, you will want to do this for appearances, but otherwise, stick to the no-space rule. As far as how many spaces between sentences or after a colon goes, some prefer two and some prefer one—just be consistent.
For examples, look at any published English writing or at this guide. Notice that there is no space between the last word in a phrase and the comma, then a space between the comma and the next word. There is a space between the opening and closing parenthesis or bracket and the words before and after respectively, but no space between the first and last words inside and the parenthesis or bracket.
If you have any ideas about how to make this guide more useful, please write to me at email@example.com. Ideas could be certain problem areas that you have overcome (and how you came to understand them), common errors that you have found as an editor, co-writer or English writing teacher of Korean scientists, or questions that remain unanswered for you that you would like to see addressed in a future edition of the guide. Also, please let me know if you found any errors in my writing so that I may correct them.
We would like to thank the writers of BiO Centre (http://bio.cc), OITEK, Inc., and NGIC at KRIBB who contributed most of the examples used in this guide, as well as conversations to help with specific issues in writing and communicating in English.