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Writing a Scientific Article
Author: ADMIN (ukstudent at gmail dot com)
Published: Tue, 22-Mar-2005
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Writing a Scientific Article. Article by Dr Maria Jackson, Medical Genetics, University of Glasgow

If you have problems with writing, a good site to visit for useful ideas on writing in general, as well as writing in biology, is the University of Richmond's Writing Centre and you can also get information on writing from the Purdue University Online Writing Lab(OWL) and the University of Ottawa Writing Centre, which also has lots of links to other relevant sites. The Online English Grammar at EduFind is another useful resource.

Using references from the scientific literature
You will see from the literature that there are many different, equally valid ways of citing references in scientific papers, but note that within a given journal one standard format is used. Thus in the Journal of Medical Genetics a numbering system is used for references and in the journal Cell the Harvard method is mandatory. How to cite your sources from UWA Library has more information on different citation styles, but note that some styles are preferred for science and other styles for arts. Two of the citation styles used in science are shown below.

Citing references in the text
All scientific information you include in your report must be accompanied by a reference to the relevant literature. Get into the habit of inserting the references into your notes or text as you write, otherwise you may forget where a particular piece of information came from. Science is based on evidence and so when you make a statement you must at the same time give the evidence which supports your statement.
Citing authors indicates that the work or ideas you describe are attributed to those authors. For general background information it is often easiest to cite reviews, as it would be impractical to cite every article ever written on the subject! But you should make clear that you are using these references as reviews (in other words the authors of the review did not carry out the scientific work themselves, merely reviewed the relevant literature). But note that for the important scientific work you describe, you should use the original source article and not a review.
Two citation styles are shown below. These are not the only methods and if you submit an article for publication in a scientific journal you will need to conform precisely to the system they advocate for their journal. Personally I prefer the Harvard style because:
• • As you read the article you get an idea of who did what and when, since author names and dates are cited in the main text.
• • If you add a reference or two at the last minute you don’t need to renumber all the references.

The Harvard Method of Reference Citation

Scientific articles you are citing should be listed, in alphabetical order by first author, in the References section of your work. You should include all authors, unless these exceed ten, in which case name only the first ten and then write "et al.". Et al. is the abbreviation for the Latin et alia, meaning “and other people”. Since et al is Latin, the words are italicized (see “The boring details” below). Note that the reference should include the full title of the paper. When citing the work in the text you use the author surname(s) and date for one or two authors [“(Hanahan & Weinberg, 2000)” in the example below], or first author surname et al and date for three or more authors [“(Thorpe et al., 1997)” in the example below]. If you cite the author as an integral part of your sentence [as in “O’Reilly et al. (1994) demonstrated that…”], then only the date is required in brackets.
Example
Cancer development is the result of a multistage process, and cancer cells have acquired a number of genetic alterations by the time they become invasive and metastatic (reviewed by Hanahan & Weinberg, 2000). Many different approaches have been used in an attempt to improve cancer therapy. For example, O'Reilly et al (1994) demonstrated that the administration of an angiogeneisis inhibitor successfully blocked cancer growth by inhibiting new blood vessel formation. Other approaches have been immunotherapy (reviewed in Thorpe et al.,1997) and the use of engineered viruses which selectively kill cancer cells (Khuri et al, 2000).
References
Hanahan D & Weinberg RA (2000) The hallmarks of cancer. Cell 100, 57 - 70.
Khuri FR, Numunaitis J, Ganly I, Arseneau J, Tannock IF, Romel L, Gore M, Ironside J, MacDougall RH, Heise C, et al. (2000) A controlled trial of intratumoral ONYX-015, a selectively-replicating adenovirus, in combination with cisplatin and 5-fluorouracil in patients with recurrent head and neck cancer. Nature Medicine 6, 879 - 885.
O'Reilly MS, Holmgren L, ShingY, Chen C, Rosenthal RA, Moses M, Lane WS, Cao Y, Sage EH & Folkman J (1994) Angiostatin: a novel angiogenesis inhibitor that mediates the suppression of metastases by a Lewis lung carcinoma. Cell 79, 315 - 328.
Thorpe PE, Wawrzynczak EJ & Burrows FJ (1997) Monoclonal antibodies and therapy. In Introduction to the Cellular and Molecular Biology of Cancer, 3rd Ed, LM Franks and NM Teich, eds.(Oxford University Press), pp.353 - 379.
Make sure it is clear who did what. Thus in the above example, if the reader wanted to find out more about angiogenesis inhibitors s/he would know to consult the paper by O'Reilly et al., whereas someone interested in gene therapy of cancer could consult the paper by Khuri et al. Don't be tempted to cluster citations at the ends of sentences (or even worse at the ends of paragraphs), when they refer to clearly different pieces of work.
So the following would be very poor use of citation:
Cancer development is the result of a multistage process, and cancer cells have acquired a number of genetic alterations by the time they become invasive and metastatic (reviewed by Hanahan & Weinberg, 2000). Many different approaches have been used in an attempt to improve cancer therapy. For example, administration of an angiogeneisis inhibitor can block cancer growth by inhibiting new blood vessel formation, and immunotherapy or engineered viruses can selectively kill cancer cells (O'Reilly et a.l,1994; Thorpe et al.,1997; Khuri et al., 2000).
When you are undertaking a project, members of a research group may tell you about their results, which are pertinent to your project, but not yet published. You can include such information in your report, and cite it as in the following example:
.... but it has been demonstrated that retroviruses will not infect this cell type (J. Smith, personal communication).

The IEEE Style of Reference Citation

Articles you are citing should be numbered in the order in which they first appear in the text. In the References section the cited works are listed in numerical order. You should include all authors in the Reference listing, unless these exceed ten, in which case name only the first ten and then write "et al.". Note that the reference should include the full title of the paper. When citing the work in the text you use the reference number. If you cite the author as an integral part of your sentence (as in “O’Reilly et al [2] demonstrated that…”], the reference number is still required in brackets.
Example
Cancer development is the result of a multistage process, and cancer cells have acquired a number of genetic alterations by the time they become invasive and metastatic [reviewed in 1]. Many different approaches have been used in an attempt to improve cancer therapy. For example, O'Reilly et al [2] demonstrated that the administration of an angiogeneisis inhibitor successfully blocked cancer growth by inhibiting new blood vessel formation. Other approaches have been immunotherapy [reviewed in 3] and the use of engineered viruses which selectively kill cancer cells [4].
References
1. D Hanahan & RA Weinberg (2000) The hallmarks of cancer. Cell 100, 57 - 70.
2. MS O'Reilly, L Holmgren, Y Shing, C Chen, RA Rosenthal, M Moses, WS Lane, Y Cao, EH Sage & J Folkman (1994) Angiostatin: a novel angiogenesis inhibitor that mediates the suppression of metastases by a Lewis lung carcinoma. Cell 79, 315 - 328.
3. PE Thorpe, EJ Wawrzynczak & FJ Burrows (1997) Monoclonal antibodies and therapy. In Introduction to the Cellular and Molecular Biology of Cancer, 3rd Ed, LM Franks and NM Teich, eds.(Oxford University Press), pp.353 - 379.
4. FR Khuri, J Numunaitis, I Ganly, J Arseneau, IF Tannock, L Romel, M Gore, J Ironside, RH MacDougall, C Heise, et al. (2000) A controlled trial of intratumoral ONYX-015, a selectively-replicating adenovirus, in combination with cisplatin and 5-fluorouracil in patients with recurrent head and neck cancer. Nature Medicine 6, 879 - 885.

Don't use someone else's citation without checking it out

In the review by Hanahan & Weinberg (above) the following statement is made: "The ultimate effectors of apoptosis include an array of intracellular proteases termed caspases (Thornberry and Lazebnik, 1998)."
Can you therefore say in your article: "The caspase group of proteases are involved in apoptosis (Thornberry and Lazebnik, 1998)."???
The answer is NO - unless you actually consult the paper by Thornberry & Lazebnik, you cannot be sure that it does in fact support the conclusion that Hanahan & Weinberg attribute to it. The scientific literature does contain errors of citation, so always check the sources you quote. Citing an article in your text should indicate that you have read that article and are therefore confident that it supports the statements you make in your own text.
See also the section below on “Theft of Scholarship” in the Plagiarism section below.

Web references

Most references you cite will be from the standard literature as published in scientific journals. An important feature of these journals is that all original research papers in them are peer reviewed. In other words, before publishing the work, the journal editors send out copies of the manuscript to two or three "referees" ie, academics who have expertise in the relevant field of science. The referees' job is to check that the work is scientifically valid before it is accepted for publication.
As part of their search for information many students use the WWW and locate web pages relevant to their topic. However, you should note that WWW pages are not in general subject to any peer review process and thus the information given may not be as scientifically sound as that obtained from a peer-reviewed journal. You may have located a page prepared by someone who has an axe to grind and is being economical with the truth. (You may need to make a judgement - who is the author? how does what they say correlate with the rest of what I know?). So, although you can get a lot of valuable information from the web, if possible you should try to find the original scientific journal articles from which the web page information was prepared. In some cases this will not be possible, and then you will need to cite the web page itself in your text and reference list, if possible with the author name and a date of publication. But be aware that the internet is an unstable resource and a page that is here today may be gone tomorrow. Or it maybe updated tomorrow to say the exact opposite of what it said today. So wherever possible use peer reviewed journals as your final references, but if you can only find the information on a web page then cite the web page in your article, but make sure the address you give is correct. Also provide the title of the Web page and the date on which you last accessed it, together with the author name(s) if available:
Haigh B, Mahbubal H & Hayden MR. Huntington Disease. From Gene Reviews at GENETests, http://www.geneclinics.org/ (last accessed 8/3/05)
In the above example the URL for the actual review article is very long and complex, so given that the authors and title of the review are available, and the article can therefore be easily located from the site homepage, it is probably best just to direct the reader to the homepage.
Note that some word processing packages will automatically format the URL address as a hyperlink and underline it – this is not very useful in a printed document, and the underlining can in fact obscure parts of the address, so best to use the “Edit > Undo Autoformat” option. If you paste in the URL, use “Paste Special > Unformatted Text” to avoid including the hyperlink formatting.
For some very large and complex sites, like OMIM, it is often preferable to give the complete URL using the actual page address, as several pages may discuss the same, or similar, genes / diseases, and you must direct the reader to the precise source of your information:
McKusick VA et al. Huntington Disease. From OMIM, http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=143100 (last accessed 8/3/05).
Do not cite search engines like Google, unless you are evaluating their usefulness or application to a problem – the URL information you cite should always take the reader to exactly the right place in the WWW – ie, the place where you got the information you are citing. Should the website URL alter (as happens from time to time) the author and title information you provide may allow the reader to relocate your source.
Do not give URLs for electronic versions of journals – even if you accessed the journal via the WWW you should give the reference to the printed (ie, paper) version.
Always check that the URLs you include as references actually do the job of taking the reader to the right place by typing them in by hand from your reference listing at a later date.

Diagrams and tables

A diagram can often be better than a long piece of prose in explaining complex events. But ensure that each figure has a Figure number, Title and Figure legend, explaining what the figure is all about, and what the reader should be looking at, particularly in the case of a photograph of a patient for example. Make sure you refer to the diagram at the appropriate place(s) in the main text. The figure, together with its legend, should be broadly interpretable without reference to the main text – it should tell a story all by itself, although obviously the reader will learn more from the main text plus the figure and legend together. It is most useful if the diagram is on the same page as, or an adjacent page to, the text that refers to it. You can:
• (OK) scan or photocopy appropriate diagrams from a book or scientific paper (but note that scanned diagrams often look fantastic on screen but appalling when you print them out)
• (better) make a drawing based on a published figure but with modifications of your own, which tailor the diagram to your report, or include new information
• (best) draw your own diagrams based on your own ideas, which may draw on sources in the literature but be quite different from anything published there
Like all other work, the sources of diagrams must be referenced; you should add the source acknowledgement(s) to the end of the Figure legend. This could take one of the following forms:
• From Hanahan & Weinberg (2000). [for a scanned or photocopied diagram]
• Redrawn from Hanahan & Weinberg (2000). [when you have produced an essentially identical copy of the original]
• Redrawn, with modification, from Hanahan & Weinberg (2000). [when you have made changes to the original, for example adding information or tailoring the diagram to your own needs]
• Compiled from information in Hanahan & Weinberg (2000) and Thorpe et al (1997). [when you have essentially constructed your own diagram from the available information]
Graphs should have a title, the axes should be labelled, and the units should be included with each axis label. Include scales in all photographic illustrations.
Like figures, tables should have table legends and their source should be acknowledged (unless of course they tabulate data you yourself have generated).

Correct use of other peoples work (or avoiding plagiarism)

As described in the above sections, it is essential that you clearly attribute all ideas, information, diagrams and text that use in your own work. To fail to do this is plagiarism. But you must also understand how to use other peoples’ text when you are preparing your own document. The crucial point is that attributing the text is not the whole story. You must also ensure that you do not use another author's form of words, or even their sentence structure as both of these are plagiarism, as illustrated below. Occasionally you may decide to quote directly from someone else's work, in which case you must use quotation marks in addition to citing the reference from which the quote was taken. Take the following extract from the article by SB Prusiner (1996) TIBS 21, 482 - 487:
"The number of cases of new variant CJD caused by bovine prions that will occur in the years ahead is unknown."
It would be plagiarism to include either of the following in your own report:
• The number of cases of new variant CJD caused by bovine prions that will occur in the years ahead is unknown (Prusiner, 1996).
• The number of new variant CJD cases caused by bovine prions that will occur in the years ahead is not known (Prusiner, 1996).
The first is a direct quote, but notacknowledged as such, and the second has used Prusiner's basic sentence structure with just a slight rearrangement and couple of word alterations. Thiskind of paraphrasing is plagiarism. The only correct methods are to use a direct, acknowledged quote (with quotation marks) in your text, or to rewrite the information in your own words.Thus:
• As discussed by Prusiner (1996), in the mid-1990s it appeared impossible to accurately predict the number of future cases of new variant CJD. (OWN WORDS)
• In 1996, Prusiner suggested that "The number of cases of new variant CJD caused by bovine prions that will occur in the years ahead is unknown" (DIRECT, ACKNOWLEDGED QUOTE)
• When nvCJD cases started to appear in the 1990s, it was impossible to predict what the future trend would be (Prusiner, 1996). (OWN WORDS)
In all the above cases the reference list must contain the TIBS article by Prusiner (1996).

Some quotes and websites dealing with plagiarism

Plagiarism: Plagiarism: what it is and how to avoid it by Gordon, Simmons & Wynn
of the University of British Columbia tells us that
"Students anxious about committing plagiarism often ask: 'How much do I have to change a sentence to be sure I'm not plagiarizing? A simple answer to this is: If you have to ask, you're probably plagiarizing."
In other words, avoiding plagiarism should not be seen simply as an exercise in altering someone else's wording until it looks "sufficiently" different. As stated by Dr Brad Fiero of Pima Community College, Arizona, you should:
"...read your sources of information, synthesize the information in your head, and then write what you know in your own unique way."
Dr Fiero also suggests that:
"If you find yourself with the source of information in one hand while you are writing your report in the other hand, then there is a good chance you are plagiarizing."
In fact the sheer number of websites produced by universities all over the world on the subject of plagiarism is an indication of the gravity of the offence of plagiarism in the academic world. For example Plagiarism by Earl Babbie, and Using Sources at the Hamilton College Writing Centre.
The University of Glasgow has its own Plagiarism Statement. If you are considered to have plagiarized (part of) an assignment you may lose all the marks for that piece of work, and other measures may also be taken.
Another website with a set of links on plagiarism is at the Purdue University Online Writing Lab (OWL). (The home page of this site has lots of other writing links which you may find useful.)
A page by Robert Harris has information on Using Quotations Effectively; in other words how best to incorporate quotes into your own text. But note that you should limit your use of quotations. Don't simply quote because you can't be bothered to write the material using your own words. Quotations should normally only be used when an author has used a particularly memorable, colourful or apposite form of words.

Theft of Scholarship

As noted earlier, you must not cite any reference that you have not read. It may be very tempting to “borrow” long strings of references that someone else has cited, but this is theft of scholarship and therefore plagiarism. For example an article by Chen et al (Am. J. Hum. Genet. 65:795{1999}) says:
"It has been documented that the allele frequencies of ADH2*2, ADH3*1, and ALDH2*2 are significantly decreased in alcoholics as compared with the general population of East Asians, including ethnic Han Chinese (Thomasson et al. 1991; Chen et al. 1996), Koreans (Shen et al. 1997), and Japanese (Higuchi 1994; Higuchi et al. 1994, 1995; Maezawa et al. 1995, Nakamura et al. 1996; Tanaka et al. 1997)."
You may think it will look very impressive to simply attach this string of nine references to your own article as follows:
There is compelling evidence from several studies of East Asian populations that certain alleles of the ADH2 and ALDH2 genes are protective against alcoholism (Thomasson et al. 1991; Higuchi 1994; Higuchi et al. 1994, 1995; Maezawa et al. 1995, Nakamura et al. 1996; Chen et al. 1996; Shen et al. 1997; Tanaka et al. 1997).
But this would be fraudulent use, particularly if you do not even read the individual articles yourself to check that they do support the conclusions of Chen et al (1999). You would be stealing the intellectual work of these authors, who carefully reviewed the available literature. It would be more honest to say:
As reviewed by Chen et al. (1999), there is compelling evidence from several studies of East Asian populations that certain alleles of the ADH2 and ALDH2 genes are protective against alcoholism.
Or alternatively, read all the articles yourself and decide for yourself what the best interpretations of the data are. Then you are in a position to honestly cite the articles. Remember that errors of citation do occur in the literature, so that theft of scholarship, apart from being sloppy technique, may lead to errors in citation in your own work.

The boring details

A well presented document is one which not only looks good in terms of overall format, but which is free from trivial errors in the text.
Make sure you have spellchecked your document, using the appropriate function of your word processor. The common complaint by students is that word processors pick up most scientific terms as spelling mistakes, even when they are correctly spelt. But you can educate your word processor - when the spellcheck function finds a word it does not recognise (for example "retinoblastoma"), you are given options which include:
• Ignore - skip this word and carry on checking
• Ignore all - will ignore every subsequent occurrence of "retinoblastoma" in your document
• Add - will add the word "retinoblastoma" permanently to the dictionary of acceptable words
If you have used abbreviations in the text, then it's best to include a "List of Abbreviations" at the start of the document. [Although some abbreviations are so commonly used (eg "DNA") that they are OK without definition]. Avoid the use of colloquial abbreviations like don't, can't etc
Related pieces of information and/or ideas should be combined into a paragraph. With very few exceptions a paragraph should not be a single sentence. Think about the structure as you are writing, and as you reread what you have written, ensuring that you have produced a sensible paragraph structure. In essays and dissertations it can also be useful to divide the text into sections with subheadings which help to orient the reader.
Try to ensure that the pagination of your report is sensible - in other words, if the sub-heading for your next section will come at (or very close to) the bottom of a page, it is best to insert a page break and have the next section start at the top of a page. Similarly, if the first line of a paragraph comes at the very bottom of a page then insert a page break and start the paragraph on a new page. Try to ensure, where possible, that figures are on the same page as the text referring to them (or at least nearby), and the Figure legend should be on the same page as the Figure. Page numbers are also useful - your word processor should be able to insert these automatically in the header or footer of the page.
Genes and proteins tend to get confused in students reports, and we often see statements like "The p53 gene causes cell cycle arrest in response to DNA damage". Obviously this should actually be "The p53 protein causes cell cycle arrest in response to DNA damage" or "The p53 gene product causes...".
Nomenclature of genes and proteins can also be a bit confusing. There are standard accepted forms of referring to a gene and the protein product of that gene. For example, in humans the RAS gene produces the Ras protein. So that the gene name is italicized while the protein is distinguished by having a capital letter and being in normal typeface. Similarly, the TP53 gene encodes p53 protein. You will find that the situation is very complex, with accepted scientific nomenclature varying from one organism to another. In some organisms the standard notation for a gene maybe italicised capitals, while the protein may be standard capitals. You should be able to see what is correct for your gene/protein system in a particular organism by looking at the literature. However, in the case of new genes and/or proteins which have been independently characterised by two or more groups there may be more than one currently acceptable name. In this case you should use just one name throughout your work, but indicate the existence of alternative nomenclature for the gene / protein.
Scientific species names such as Saccharomyces cerevisiae should be italicised, while the common name, yeast, is not. For restriction enzymes, the first 3 letters (which are derived from the species name of the bacteria from which the enzymes originally came) are italicised, and the remaining letters are, in general, upright.
Latin words like in vitro, in vivo, de novo, in situ are italicised.

Punctuation

Getting the punctuation wrong can completely change what the reader understands from your text.
Try the Eats, Shoots and Leaves punctuation quiz.
More advice on punctuation can be found at the University of Richmond's Writing Centre and the Purdue University Online Writing Lab(OWL).


© Copyright for this article belongs to Dr Maria Jackson

Re-Printed with the Kind Permission of Dr Maria Jackson. Original article, with hyperlinks to source material at: http://www.mblab.gla.ac.uk/~maria/MedGen/SciWri.html



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