Scientific Writing

From http://www.biojobblog.com/

How to write papers that people will read: A mixed bag of stuff!

Sources

You can start with

• Never finish with it! Note it is not (and never will be) peer-reviewed
• e.g global warming
• Where do the figures come from?
• but here is the important link
• Hansen, J., et al. (2006) "Global temperature change". Proc. Natl. Acad. Sci. 103: 14288-14293

Writing Science

• Do you want people to read your work?
• Do you want to be understood?
• Do you want your ideas to be taken seriously?

• Edit your own writing by asking yourself
  • Was my message clear?
  • Could I have used simpler language?
  • Did I eliminate awkward passages or phrases?
  • How could I have shortened it?
  • Did I use an active voice?
  • How can I improve it?

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  Plagiarism

  Stolen from webee.technion.ac.il Prof Keider, Technion

  How to use other peoples work

  • Deliberate Plagiarism:

  • Downloading an essay, changing the name of the author and submitting it as your own.
  • Downloading 10 essays, taking paragraphs from each one and submitting it as your own.
  • Hearing about someone's idea at a conference and then submitting it as your own. (Theft of intellectual property)

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  Accidental Plagiarism:

  mostly
  • Always acknowledge your sources
  • Err on the side of acknowledging too much.
  • Exact format doesn't usually matter in this course: I suggest that you name the source in the body of the paper, with a footnote to the exact place.

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  Plagiarism

  What follows is plagiarized from the library website!

  Plagiarism is defined by the Merriam-Webster Dictionary as "the act of stealing and passing off the ideas or words of another as one's own."

  What that means for you as a student is that if you do not use footnotes, endnotes, or bibliographies properly when submitting assignments, you too may be accused of plagiarism. According to Carleton University's Academic Regulations,(section E. 14) anyone caught plagiarizing has committed an instructional offence. Students found guilty may be: 

  a) expelled; 
  b) suspended from all studies at the University; 
  c) suspended from full-time studies; 
  d) awarded a reprimand; 
  e) refused permission to continue or to register in a specific degree program but subject to having met all academic requirements shall be permitted to register and continue in some other program; 
  f) placed on Academic Warning; 
  g) awarded an F or Abs in a course or examination. 

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  Many students think that as long as they write things in their own words, they don't need to acknowledge the original source. This is not true! Any information that is not an original idea of your own, that you get from another source, needs to be noted. In a research paper there are 2 main ways of incorporating other people's ideas

  Direct quote: This is used if you are including the exact words used in the written source. If it's a short quotation, you usually incorporate it directly into your sentence and use quotation marks around it. If it is longer, you usually set it out in a block of text, indented from the rest of your text, without quotation marks

  Paraphrasing: This is when you use your own words to express ideas you have read about. In this case, you still need to acknowledge the source, even if you aren't using a direct quotation. 

  How to acknowledge the source? 

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  Okay, so now you know that you have to somehow give credit to your sources of information. The way you do this may depend on what discipline you are in or on what citation style you are using. In general, you usually acknowledge the source both within the body of your text (usually very brief information such as author and year, or footnote/endnote number), and then also in a fuller bibliography at the end of the paper (This listing is much more detailed with author, title, date, page...) There are a number of different styles used in academic writing. The one you use will be determined by one of the following:
  • your professor may tell you what style to use
  • your department may have a preferred style
  • you may be allowed to choose the style you want to use (in NSCI 1000 we have no strong requirements)

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  Some of the more common styles used are APA style (American Psychological Association), especially in the social sciences, and MLA style (Modern Language Association ) , often used in the Humanities. The important thing is that you should be consistent: use the same style throughout your paper. 

  Some examples

  • According to Jane Doe , "Excessive use of snowboards may lead to permanent spinal damage, especially in those under 18 years of age." (12)

  In this example, a footnote or endnote number is used, which points the reader to a list somewhere which will provide the details of the information source

  • Students who live away from home spend almost twice as much on alcohol as those who live with their parents (Smith, 2001)

  In this example, the author and year of the source are indicated in parentheses at the end of the sentence containing the paraphrased information. Again, a full list at the end of the paper will give more detailed information on the source

Referencing Guidelines for Science

Sometimes you may be unsure if a reference is required. The general rule is, "When in doubt, reference it". If you had to look up the information you are putting in a report, then where you found that information should be referenced. One standard format is

• Sugars bearing anomeric carbons whose hydroxyl groups have not formed glycosidic linkages are termed reducing sugars, since they readily reduce mild oxidizing agents (Voet et al., 2000). Notice that " et al." is used in the citation because there were more than two authors. For one author it is simply (Smith, 1999), two authors is (Smith and Pierce, 1998). Don't forget to reference your figures too:

  Sucrose α-glucose + α-fructose Figure 2: The invertase-catalyzed hydrolysis of sucrose to form glucose and fructose (Stanford University, 2003).

Notice that Stanford University is cited (not the website). If there had been an author's name on the website, that would be cited. An example of a properly formatted bibliography that contains references for websites, lab manuals, textbooks and journal articles is as follows:

• References
  • Carleton University. 2002. Biochemistry 63.305 Practical biochemistry 2002-2003. Carleton University Press, Ottawa. pp. 68-72
  • Jones, M. (2000). Organic chemistry. Second edition. W. W. Norton & Company Ltd. New York. pp. 858-860
  • Matic, I., F. Taddei and M. Radman. (2000). No genetic barriers between Salmonella enterica serovar Typhimurium and Escherichia coli in SOS-induced mismatch repair-deficient cells. J. Bact.. 182(20): 5922-5924
  • Stanford University (2003). Analysis of Foods for Starch and Vitamin C. http://www.chem.csustan.edu/CHEM2000/Exp8/bkg.htm (Apr 6, 2003)
  • Voet, D., J.G. Voet, and C.W. Pratt. (2002). Fundamentals of biochemistry. Upgrade edition. John Wiley & Sons, New York. pp. 200-204
• An excellent tool that can help in figuring out proper referencing format for some of the trickier electronic resources is The Columbia Guide to online style: http://www.columbia.edu/cu/cup/cgos/idx_basic.html

• What if you don't know the source?
• Usually It is well known that the whale is not a fish or It is widely believed that it rains more in winter than in summer.
• Don't use either of these constructions too often, or you'll just look lazy! If it is an idea that is in many places, you can give an example
• The kinetic theory of gases gives a direct link between the energy of gas molecules and the temperature (see, e.g., Giancoli, Basic Physics).
• a rule of thumb: if something is less than 20 years old, refer to the original article. If it's more than 20, chances are it is well known. But be careful

• Carleton University's Writing Tutorial Service includes links to: 
• Writing Handouts and in particular:
• Quoting and Paraphrasing
• Citation Links: these are links to books and Web sites that will illustrate the various citation styles 
• Citing Electronic Resources 
• Style Manuals, Essay and Thesis Preparation This gives you descriptions and call numbers of books in the Library that help with style and citation. 
• How Not to Plagiarize
• How to Use Sources and Avoid Plagiarism
• Information Ethics for the Informed Consumer
• Plagiarism.org
• Plagiarism: What it is and How to Recognize and Avoid it
• Turnitin.com This is just one of the services available to professors for catching students who plagiarize 

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Mechanics

so how do we write the paper? Up to 1990 (roughly)
1. Write the paper in long-hand
2. Get someone to type it
3. Send it to the journal
4. Journal employs type-setters, give you draft
5. You correct the draft
6. Journal re-employs type-setters, give you a finished product
7. Problems: Slow, at least two sets of transcription (with associated errors), expensive
Now most journals demand camera-ready copy: much faster, but you need a sophisticated set of tools

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Tools

Text

• Some journals will let you send in MS-Word files (.doc) or Rich-Text Format (.rtf files)
• Good for papers with a few, short equations.
• Most powerful (since infinitely extensible) is TeX: type-setting language. (pronounced Tech: go figure!)
• Free editors available (Search for LaTeX for Windows or Mac)
• Huge free support system
• Steep learning curve (but EVERYONE starts from sample files).
• Need templates
• Hard to read actual TeX files
e.g.

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Plotting Graphs

You can plot them by hand, scan the results but the journal won't take them.
• Plotting software widely availoble: e.g most spreadsheet programs (Excel, Open Office ... )
• Statistical packages (SPSS, R, )
• Specialist packages (ProFit, Sigmaplot) are much more flexible.
• Plot is free for Mac, or try http://www.fileguru.com/apps/plot_curve
Putting in formulae

Mathtype is industry-standard,( reduced versions included with various word-processors)

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References

• We have about one million articles per year. How do you find the one you read three years ago.....?
• Firstly (if possible) download the file on your own computer (usually .pdf file from journal
• Need a info manager. Very good (and free) but ugly is Bibtex: integrates with TeX
• Good interfaces via BibDesk for Mac
• or BibDB for Windows.
• Not free, but more user friendly, is Endnote
• can use these to include links to your own files
• with a Latex processor, have automatic integration with BibTex (i.e. don't need to shift references around

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the results:

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Bad Writing and how to avoid it!

Well, I've got Microsoft Word and that catches al the grammatical errors... Peer edit: Most good writers recognize the value of a second opinion. Because writing is so personal, we commonly get too close to our work and have a hard time seeing our own mistakes. What may seem clear and simple to you, may be ambiguous and complicated to someone else. Sometimes a different viewpoint can make all the difference.

Authors

Usually, a paper will have more than one author:

e.g. OPAL Collaboration

Physics Letters B Vol: 490, Issue: 1-2, September 28, 2000 pp. 71-86

A measurement of the rate of charm production in W decays

Authors:

• How do you decide who goes on it?
• How do you decide what order they go in?
• Do you put students on? (even if they have only just started?)
• Do you put technicians on?
• Do you put people who contributed at the beginning, but dropped out or moved on elsewhere>?
• Do you put dead people on?
• DO you put the authors in alphabetical order?
• Do you put people on in terms of seniority?
• Do you put people who are essential to the project but haven't contributed to the science (e.g director of a lab)?

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Usually each field will have its own convention. In physics, usually:
1. Only people who have actually worked on the experiment.
2. Alphabetical order except
   • If one author has contributed much more than the others
   • If one author is giving a talk on it
   • If the paper is a major part of a student's thesis
   Note that many journals now have a policy that each author must sign a disclaimer that they have contributed to the research and that they are in agreement with the conclusions.

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Acknowledgements

In any paper, you've probably had help or conversations with people. You are also usually funded by some group, and you may have visited somewhere while you were doing the work. The above rule applies: err on the side of too much credit! However, we can always run into problems!
• Hi

  I was reading your recent paper hep-ph/0406308 and I think that it would be fair to include in your reference list my paper PLB436(1998)257, with Arkani-Hamed, Dimopoulos and Dvali, (appeared a few weeks after your ref.[1]), which contains the first string realization of low scale gravity models.

  I would also like to bring in your attention my paper Nucl.Phys.B516(1998)70 (with Dimopoulos and Dvali) where we discussed submillimeter forces in theories with large extra dimensions prior to the other references.

  Sincerely, I. Antoniadis

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now lets try our hand at actually editing a document:
1. this is what we start from
2. this is what we end up with