Talk:Scientific writing

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The following text is being copied over from Wikipedia where it was removed as being unencyclopedic. The text could still be quite valuable as a how-to guide. Clifflandis 20:01, 1 May 2010 (UTC)

Style of writing and use of English in essays and scientific papers
Scientific writing is the basis of going to institutions, libraries, and universities to gain information and present it in a concise manner abiding to the generally accepted template of most scientific papers. The scientific format used to acknowledge bibliography resources is CSE. The following advice may be of help to students writing an essay or a scientific paper.

Three aspects of style seem to cause problems


 * 1) Division of the text into sentences and paragraphs. Sentences should have only one idea or concept. In general, sentences in scientific prose should be short, but full stops should not be added so liberally that the writing does not flow. The use of paragraphs helps the reader to appreciate the sense of the writing.
 * 2) Superfluous phrases and words should be avoided. Do not write phrases such as "It is also important to bear in mind the following considerations". Most woolly  phrases can be omitted or replaced by a single word.
 * 3) Try to use familiar, precise words rather than far-fetched vague words. For example, "cheaper" may replace  "more economically viable."

A good style is helped by logical planning. Decide what you want to write, then write it simply and in a sensible order. Put the first draft away for a few days and then rewrite it.

Tense and mood
Write in past tense unless you are describing present or future situations. Use the active voice rather than the passive voice. For example, instead of writing "The food was eaten by the pig", write "The pig ate the food". The active voice is easier to read and reduces the sentence length; this is particularly important, since most scientific journals have a word-count limit. Indiscriminate changes in tense are confusing and can give meaning to a statement which does not accord with the facts. However it can be acceptable to write in more than one tense in the literature review e.g. "Brown  (1995) showed that the brain is more fully developed at birth than other organs". In this case the present tense can be used for the second half of the sentence because it gives knowledge that is universally accepted. Materials and methods should be written in the past tense. "The experiment was designed in the form of a 6 x 6 Latin square." Remarks about Results should mainly be in the past tense. "When a high protein diet was fed to rabbits they grew rapidly." Any conclusions drawn should be in the past tense, e.g. Pigs in this experiment grew most rapidly when fish meal was added to their diets. When referring to the conclusions of a particular experiment, it is incorrect to state pigs grow most rapidly when fish meal is added to the diet.

However, for the mathematical sciences, it is customary to report in the present tense.

Sentence construction
The purpose of any paper is to convey information and ideas. This cannot be done with long involved sentences. Keep sentences short, not more than 30 words in length. A sentence should contain one idea or two related ideas. A paragraph should contain a series of related ideas.

Choice of words
Words have precise meanings and to use them correctly adds clarity and precision to prose. Look at the following pairs of words that are often used in scientific texts. Learn how to use them correctly: Fewer, less; infer, imply; as, because; disinterested, uninterested ; alibi, excuse ; data, datum; later, latter; causal, casual; loose, lose; mute, moot; discrete, discreet. Example to show difference between less and fewer by using the two words in the same sentence. Less active blood cells Fewer active blood cells Use a standard dictionary and Roget's Thesaurus of English Words and Phrases to find the correct meaning of words.

Use of pronouns
When you write ‘it’, ‘this’, ‘which’ or ‘they’ are you sure that the meaning is plain? A pronoun usually deputizes for the nearest previous noun of the same number (singular or plural) - The cows ate the food; they were white. The cows ate the food; it was white.

Correct spelling, including the use of plurals
Some words have alternative spelling e.g. tyre, tire, grey, gray; draft, draught; connexion, connection, plow, plough, often the difference is between the American and British spelling. In other cases an apparent misspelling is a misuse of a word e.g., principle and principal; practice, practise (The former is a noun, the latter is a verb) The plural of many words in the English language is achieved by adding an s (or es) to the single. For example car becomes cars and potato becomes potatoes. However some words have the same form in both the singular and plural. For example sheep - there is no such word as sheeps. Other words are already plural such as people and equipment, so don't use peoples (unless you are referring to different groups of people or different ethnic groups) and equipments. Adopted words sometimes take on the plural of the original language, for example datum becomes data and fungus become fungi.

Use of abstract words
Use the concrete and not the abstract to achieve clarity and precision. "Cessation of plant growth operated in some of the plots." Obviously a cessation cannot operate (Some plots of plants did not grow during the trial) The abstract noun basis is commonly overworked. "Measurement of storm intensity involves recording staff to be available both day and night on a 24 hour basis." "To measure storm intensity, recording staff have to be on duty throughout the day and night."

Be careful with the use of the present participle (Gerund)
Having said that the cow stood up. After standing in boiling water for an hour, examine the flask. The gerund always ends in 'ing.' If the sentence is left without a subject (a hanging participle) then the action of the verb is transferred to the object of the sentence (first sentence) or to the person taking the action (second  sentence).

Misuse of emotional words (avoid)
One cannot develop a logical argument using emotional words: e.g. progressive, reckless, crank, sound, good, correct, terrorist, freedom fighter, insurgent, sexist, imperialist, improved, superior, deviationist, fascist.

Superlatives
Very, more, much, have a place when used economically. As superlatives they are out of place in scientific writing. Superlatives such as gigantic, earth shattering or fantastic should never be used.

Qualifying the absolute
Some adjectives are absolute and cannot be modified such as: sterile or unique. Other adjectives, such as "pregnant", have to be qualified with care. A petri dish is either sterile or not sterile. It cannot be very sterile, quite sterile or fairly sterile; An object is  unique, and although a woman can be recently pregnant, she can not be slightly pregnant.

Loose expressions (avoid)

 * Bulls with a high milk yield tend to have fat percentages below average. Do bulls produce milk?
 * Ewes were fed on a pregnant maintenance ration. Clearly the ration was not pregnant.
 * In each selected village 30 farmers were interviewed, namely 10 large, average and small farmers. Is the reference here to the size of the farmers or to the size of their farms?

Grandiloquence (Examples quoted by J Oliver (1968))
Avoid the use of scientific jargon. The aim in scientific writing is to inform using simple language not to confuse by the use grandiose sounding words and phrases.
 * Grandiloquent phrase: The ideal fungicide ... must combine high fungitoxicity with low mammalian toxicity and phytotoxicity, and with an absence of tainting or other deleterious side effects when the fruit is processed.
 * Simple replacement: The ideal fungicide ... must kill fungus effectively, but must be harmless to animals and plants, and must cause no tainting or other harmful side effects when the fruit is processed.
 * Grandiloquent phrase: The phenomenon can be macroscopically observed upon laparotomy.
 * Simple replacement: Visible to the naked eye on opening bird's cavity.

Genteelism
"I" is not immodest in a research worker and therefore use it (although not to excess) NOT "The present writer" or "The author of this communication".

The Misuse of the definite article "The"
Avoid Overuse of the Word "the" Only use when it applies to a particular item that has been referred to before, e.g. 'the various patients' may have been mentioned before. All others could be omitted.

The excessive use of the pronoun "it" in a sentence
Avoid excessive use of the indefinite pronoun "it".
 * "It would thus appear that" can be replaced by "apparently";
 * "It is evident that" by "evidently";
 * Other commonly used phrases such as: "It will be seen that"; "It is interesting to note that" and "It is thought that", can be left out without any meaning being lost.

Avoid verbal obscurantisms and use simple words
Always say what you mean NOT for example: Some phrases show sloppy thinking. For example, the phrase 'It has long been known that' usually means that the writer has not bothered to look up the reference. Correct to an order of magnitude probably means that the answer was wrong. Almost reached significance at the 5 % level usually means a selective interpretation of results. Text is easier to understand if simple words and phrases can be used to replace more complex or foreign ones. For example ameliorate can be replaced by improve; analogous by similar ; anthropogenic by human; Ceteris paribus by other things being equal; component by part; ingenuous by innocent; ingenious by clever; inter alia by amongst other things; utilise by use; Prima facie by at first glance; remunerate by pay; terminate by end; pari passu by at the same rate, pace or time and peruse by read.

Colon and semi colon
A colon is used when a list or explanation follows, a semi colon is used to separate two or more related clauses provided each clause forms a full sentence. Note its use in the sentence below and in the section above on choice of words.

The apostrophe
These are used either to indicate the absence of a letter e.g. isn’t it (for is not it) doesn’t (for does not). Note the difference between (it is) it’s a boy and its, which is the possessive adjective of it (everything in its place) or to denote possession (the boy’s bike). If a word ends in s, the apostrophe may be placed after the s and the final s omitted (the calves’ eyes).

Commas
Examples of the most important uses of commas in scientific writing are given below. A comma is put in a sentence to denote a brief pause between groups of words:
 * I will show you the paper about which I was speaking, but it is not as useful as I first thought.

Or to separate subclauses:
 * Professor Brown, who is in charge of recruiting for the University, said that the latest estimates were higher than those for this time last year.

Finally to separate all items in a list except for the last two;
 * The following items may be imported duty free into Azania: Animals, cereals, plants, fruit, trees, legumes and nuts.

Observe the importance of the comma paced between fruit and trees in this particular list.

Other points concerning the use of English
One mistake commonly made, particularly by students whose first language is not English, is to not match the verb with the noun. A singular verb must always be associated with a singular noun, and similarly a plural verb with a plural noun, although a number of exceptions exist where a singular noun is used in a plural sense (for example, ‘number’ in this sentence) or, less commonly, a plural noun is used in a singular sense (for example, ‘headquarters’), and the verb then can, and usually should, agree with the sense of the noun's usage. Difficulties arise especially with nouns which do not end in ‘s’ in the plural form. For example livestock and data are plural.

Numbers and Units
Quantities should be given only as many significant figures as can be justified. For example the metabolic rate of an animal should not be quoted as 326.18W if it can be measured to only within about 5 %. It should be written as 330W.

The figures within a number should be grouped in threes (with a small space between each group) so that they are easier to read. Commas should be avoided. For example: 21 306.1 not 21,306.1

Some require units, and the Systeme International (SI) should be used where possible. Some common units and their abbreviations are given below. The full stop is not used in the SI system.

When incorporating statistical data into the text, the test used (eg chi squared) should be included, along with the degrees of freedom, the calculated value and the P value.

The layout of a scientific paper
Many people find it difficult to write a scientific paper. The aim of this article is to help even the most uncertain writers to produce a clear and well presented piece of writing. The layout for a scientific paper is normally:
 * A title,
 * An abstract,
 * An introduction (which is made up of a brief literature review),
 * Materials and methods,
 * Experimental,
 * Results,
 * Conclusions,
 * Acknowledgements and a
 * List of references.

How to start a scientific paper
Specialized scientific reviews and books may provide a good introduction to the subject. They will also contain additional references, some of which may be published in journals that are available in the local libraries. A good knowledge of existing information is essential for anyone in scientific research. Sir Isaac Newton said: Scientists have saved some of the labour of observation and experiment by accepting information already in the literature as a starting point. However statements in published articles are not necessarily true, and are seldom the whole truth because: A scientist should critically review the available literature, and determine any modifications that might be necessary. The relative usefulness of various types of paper and publication is given below. The low numbered references are useful as background reading and to provide an overview of the subject. The higher numbered sources, particularly 8, 9, 10 and 11, provide accurate and up-to-date information.
 * I can see further because I stand on the shoulders of giants.
 * Subjects have seldom been studied exhaustively.
 * Recent advances in technique or design of experiments may lead to additional observations.
 * These may lead to a different interpretation of results.
 * Therefore new enquiry may be needed.

Sources of information that may be consulted in the preparation of a literature review on a scientific subject
There are a large number of sources of information that can be used to find the relevant information, can be used to write an essay or to write a scientific paper. Some of the information sources are less reliable than other sources. Information from popular sources tends to be less reliable than information direct from scientific papers because it is second or third hand. The list below indicates the usefulness of the various sources available: From 1 the most popular to 11 most scientific, up to date and reliable:
 * 1) 	The World Wide Web.
 * 2) 	Scientific textbooks.
 * 3) 	Newspaper articles, articles on science subjects in popular journals.
 * 4) 	On-line journals (not refereed).
 * 5) 	Popular science journals, e.g. New Scientist. http://www.newscientist.com
 * 6) 	Review articles in scientific journals (e.g. Nutrition Abstracts and Reviews or in 'Trends' journals such as Trends in Plant Science). http://www.trends.com
 * 7) 	Grey literature (i.e. information not readily available), for example, conference proceedings, research reports, annual reports.
 * 8) 	Abstracting journals, e.g. Grassland and Forage Abstracts, Veterinary Bulletin http://www.cabi.org; Databases containing annotated bibliographies (e.g. by CABI).http://www.cabi.org ,On-line-searching of database titles; Current contents.
 * 9) 	Science citation index.
 * 10) 	Higher degree theses.
 * 11) 	Scientific papers in scientific journals (including refereed on-line journals).

Titles for essays and scientific papers
The title should indicate what the essay contains and be as concise as possible. Sacrifice brevity for clarity. The title should be a concise summary of the paper. Include important nouns or key words and then join together within the title. Examples 'The limitations of maize(corn) as an energy source in diets for children', or 'The feeding of rice straw and sorghum tops with molasses and urea to cattle'. Key words: Maize, corn, humans, diets, rice straw, sorghum, molasses, urea, and cattle. When an essay or a paper is being written, an author should constantly refer back to the title to ensure that what is being written is encompassed by the title. J. Oliver, in his book on scientific writing (written in the 1960s), quotes an example where he was looking for paper on 'Acknowledgements'. He could not find it in the indexes because the paper was entitled Independence in Publication. In other words the keyword 'acknowledgements' was missing from the title. This type of problem is less likely to arise today because most searches today are made electronically on databases. These searches include searches of keywords words included in the abstract as well as those in the title. It is highly probable that the word acknowledgments would have occurred in the abstract and he would have found the paper for which he was looking. Unconscious humour or inaccuracies should also be avoided in titles, e.g.one quoted by J.Oliver : Freezing and storage of human semen in 50 healthy medical students. (It is to be hoped that the medical students remained healthy and fertile after such an experiment). Various types of title can be used for a paper:

Job title
Indicative titles indicate the subject matter of a paper but give no indication of any results obtained or conclusions drawn e.g. The effectiveness of bed nets in controlling mosquitoes at different seasons of the year.

Informative titles
Informative titles give an indication of results achieved and conclusions drawn as well as the subject matter of the paper e.g. Bed nets control mosquitoes most effectively when used in the rainy season.

Question-type titles
This type of title obviously asks a question. e.g. When are bed nets most effective when used to control mosquitoes?

Main-subtitle (series) type
This type of title indicates that there is a series of papers on one subject. This approach is not liked by editors of scientific journals because if they accept the first paper they will be duty bound to accept sequels. e.g. The effect of bed nets on mosquitoes: 1.Their effectiveness when used only in the rainy season.

Hanging titles
Called a hanging title because it appears to be the first in a series without actually saying so .e.g. ''The effect of bed nets on mosquitoes: Their effectiveness when used only in the rainy season. ''

How to write titles
Ensure that the title:
 * Describes the contents of the paper.
 * Is accurate, concise and specific.
 * Has as many key words as possible and is modelled on the style adopted by the publication for which you are writing.
 * Is as easy to understand as possible.

The title should not: In most cases when writing a title of a scientific paper the title should be followed by the author's name and full address of the institution where the work was carried out. If an author has moved, his/her new address should be added as a footnote.
 * Contain a full stop, unless it is an informative title
 * Contain unnecessary words such as "Some notes on....……. "An investigation into..……..
 * Contain abbreviations, formulas and acronyms
 * Promise more than is in the paper
 * Be too general

How to write abstracts
The abstract should be used to bridge the gap between the title with a few words and a paper of several pages. Remember that the abstract will be read by more people than the paper itself.

An informative abstract
An informative abstract contains a summary of all the main points that are in the essay or paper. To prepare an informative abstract an author should read the essay or paper, making notes as he or she progresses.

An indicative abstract
An abstract for a book is normally written as an indicative one. In other words it tells you what subject matter the book covers and is not a summary of all its contents. Abstracts should not contain: References to tables or figures, because these appear only in the paper; abbreviations or acronyms unless they are standard or explained; References to literature cited; any conclusions that are not in the paper itself.

Introduction
An introduction to a scientific paper should normally  not  exceed 400 words (check the requirements of the Journal to which you intend to submit your paper) and it should cover the following subjects:
 * The background to the subject to be investigated,
 * Give a brief resume of what is the state of present knowledge about the subject to be investigated quoting the appropriate references.
 * Identify gaps in existing knowledge
 * Explains the reason for the current investigation

Materials and methods
This section should deal with four main topics:
 * Equipment and materials used
 * Experimental design
 * Observations made
 * Methods of analysis used, statistical (and chemical if required)

Results
This section should contain: NB. The data presented in tables, and graphs should be understandable without reference to the text and the text should be clear without reference to the tables and graphs
 * The information which the investigation has provided
 * Tables and graphs which summarise the data collected
 * Text used to draw attention to the main features presented in the tables and graphs

Discussion and conclusions
This section should summarise the main findings of the experiments undertaken
 * Should compare these results with the results of other workers in the same field
 * Should draw reasoned conclusions
 * Should compare these conclusions with those drawn by other workers
 * Should indicate the practical implications of the findings
 * Should indicate what further research is needed

Acknowledgements
These should be clear and any help of academic, scientific or technical nature should be acknowledged. But if the acknowledgement is overdone there is a danger that the reader will wonder what contribution the author made to the paper. For example: 'I wish to thank Dr. Lester, who not only suggested most of the experimental design but also greatly helped with the interpretation of the results, Dr Brown who contributed greatly to the writing of the paper and Mr A.S.Brown who carried out most of the experimental work'.

Tables and graphs in scientific papers
Tables should be numbered in a continuous sequence through the essay. Each table must be referred to in the text, but it may also have a heading clearly showing its content. The units of any numbers in the table must be clearly stated. If the table was synthesized from data published in previous publications these references must be cited. The inclusion of a large number of tables makes the text difficult to read and should be avoided. Sometimes data can be more clearly presented as graphs rather than tables. Tables should be put in an appendix if they are relevant but not essential for an understanding of the text. Tables should be clearly understandable without reference to the text and vice versa. The text should be used to explain the main parts of a table. Graphs and other figures should also be numbered sequentially. Each must have a self-explanatory heading, and must be referred to in the text. The axes of graphs should be clearly labelled and must give the units.

Citation of reference in the text
Reference may be cited in two ways. Either "Brown, Smith and Jones (2006) and Abdulahi (1998) confirmed these results..." or "These results were confirmed by similar experiments (Brown, Smith and Jones,2005; Abdulahi, 2006)".

The names of all the authors (but not their initials) should be given the first time the reference is cited in the text. If there are four or more authors, an abbreviation of the forms "Brown et al. (2001)..." should be used for subsequent citations. Where more than one reference is used for the same author in one year, lower case letters should be used to distinguish between them, for example, "McLean (2002b)".

List of references and end of paper
The reference section contains a list of all the references cited in the text. References should be arranged in alphabetical order (according to the name of the first author). Each reference to an article should contain the following: For example:
 * 1) Name (or names) of author(s), (each) followed by initials.
 * 2) Year of publication in parenthesis.
 * 3) Title of article.
 * 4) Title of journal, either in full or abbreviated according to the World List of Scientific Periodicals.
 * 5) Volume of journal, underlined
 * 6) Number of first and last pages of articles.


 * Hutber A.M. and Kitching R.P. (2000). The role of management segregations in the control of intra-herd foot and mouth disease. Tropical Animal Health and Production,  32: 285-294

Each reference to a book should contain:
 * a) Name(s) and year, as above.
 * b) Title of book. The most important words in the title should be given in capital letters e.g. Milk and Beef Production in the Tropics (N.B. this applies to the titles of books only).
 * c) Publisher and place of publication e.g. Oxford University Press, London

Each reference to an article which is published in a book or Conference Proceedings should also contain the title of the book and its editor. For example:


 * Chalmers, E.E. (2004). Advantages and disadvantages of nomadism with particular reference to the Republic of Sudan. In: Beef Cattle Production in Developing Countries (ed. Smith, A.J.), pp. 388-397. Centre for Tropical Veterinary Medicine, Edinburgh.

Attention should be paid to uniformity of punctuation. Please check the list of references, since it is very frustrating for the reader to find that references in the text are not included, or that they are wrongly quoted. Make sure that references in the text are in the reference list - Programs such as Word, Papyrus, and Endnote can assist with this chore and that of putting references in order.

A good starting point is a classic textbook The Elements of Style originally written and privately published by Cornell University professor William Strunk Jr. in 1918.

=Technicalities=

Typesetting

 * WYSIWYG (What You See Is What You Get)
 * Microsoft Word - versatile commercial document composing tool. Nevertheless it does have 1 very important inherent drawback: equations quality.
 * OpenOffice.org - ...


 * WYSIWYM (What You See Is What You Mean)
 * LaTeX - a macro package around TeX, which is a typesetting system capable of providing truly high-quality material of any kind
 * LyX - Open source document processor used to create WYSIWYM documents