Scientific Writing & Referencing CSE Style

1. Scientific Writing & Referencing: CSE Style: Vanessa Couldridge Scientific Writing & Referencing CSE Style BCB 703: Scientific Methodology Scientific Writing & Referencing: CSE Style Vanessa Couldridge Please note: there is NO AUDIO for this chapter

2. Scientific Communication Scientific Communication Primary Scientific Paper Primary Scientific Paper Technical Paper Thesis or Dissertation Review Article Book Popular Article Conference Talk Conference Poster Web Document Press Interview and Other Media

3. Sections of the Paper Sections of the Paper • Figure legends • Tables • Figures • Title • Abstract • Introduction • Materials and Methods • Results • Discussion • Acknowledgements • References

4. Title Title • Must be carefully worded • Needs to be informative • Should not be overly long • Should contain important key words so that others will find the paper when doing literature searches on the topic • Try to catch the reader’s attention

5. Abstract Abstract • Brief summary of a paper • Indicates what the aim of the study was and what the main results and conclusions were • There may be a limit placed on the number of words allowed, so write concisely • Contains no citations • Often people will only read the Abstract of a paper, so make sure it is worded carefully • Usually easier to write the Abstract last

6. Introduction Introduction • Introduces the topic of research and supplies the rationale for the study • Summarise previous research in the field and explain how your study will build on this • Include relevant background information on the species or area you are studying • Start with broader issues, then move to more specific topics • At the end of the Introduction, briefly state the objectives of the study

7. Materials and Methods Materials and Methods • Detailed explanation of experimental protocol: • How? • Where? • What equipment? • What statistical analyses? • Someone reading this section should be able to exactly replicate your experiment • Can be divided into sub-headings

8. Results “The great tragedy of Science – the slaying of a beautiful hypothesis by an ugly fact” T.H. Huxley Results • Remember: The absence of differences between treatments can still be a significant result

9. Results (continued) Results (continued) • Present the outcome of the experiment, without providing any interpretation • Use tables and figures to summarise results • Legends should provide enough detail so that tables and figures can be understood without reference to the main text • Be careful to include all necessary information when reporting the results of statistical analyses • Can be divided into sub-headings

10. Discussion Discussion • Purpose is to interpret your findings • Begin by briefly recapping the main results • Explain what these results mean, in light of the previously stated objectives of the study • State whether your results support or contradict previous studies. If they are contradictory, suggest why this might be? • Mention possible shortcomings, but do not belabour them

11. Discussion (continued) Discussion (continued) • Explain the relevance of your results in terms of the “big picture” • Suggest possible directions for future research

12. Acknowledgements Acknowledgements • Unless you did everything yourself, using your own equipment and supplies, paid for all costs out of your own pocket, and your study was carried out in your own building and/or on your own land, you will need an Acknowledgements section in your paper • Thank people or institutions that provided: • Funding • Access to field sites or samples • Technical, intellectual, or other help

13. Citations in the Text Citations in the Text • Every idea or finding that is not your own must be acknowledged by a citation • Include the surname of the author(s) and the year of publication e.g. Algae are extremely diverse in their morphology (Smith et al. 2006; Jones & Green 2002). • If the author’s name forms part of the sentence, give only the year of publication. e.g. Smith (2002) found some species of algae to occur in arctic sea ice.

14. References References • Check carefully that all citations in the text appear in the reference list and vice versa • Pay attention to the formatting details specified by the journal you are submitting to • In general: • The list is alphabetical by the first author’s name • When first authors have the same name, sequence by the second author’s name • If you have papers with identical authors, sequence these chronologically

15. References (continued) References (continued) • Example: Journal Article: Author, A.B. 2006. Title of article. Title of Journal. 100:1-5. • Example: Book Author, A.B. 2006. Title of Book. Publisher: City. • Example: Chapter in a Book Author, A.B. 2006. Title of chapter. In: Editor, C.D. (eds) Title of Book. Publisher: City. Pages 1-20. • Example: Website http://www.scientificmethodology.com (Accesed on 03-04-2006 at 09h00)

16. Writing Tips: Style “beauty of style and harmony and grace and good rhythm depend on simplicity” Plato Writing Tips: Style • Use words that are: simple, essential, specific, familiar • Always try to be as clear and concise as possible

17. Writing Tips: Paragraphs Writing Tips: Paragraphs • Topic sentence • First sentence • States what the paragraph is about • Supporting sentences • Make up the body of the paragraph • Discuss the issue presented in the topic sentence in more detail • Concluding or connecting sentence • Allows the paragraph to flow logically into the next one

18. Writing Tips: Paragraphs (cont.) Writing Tips: Paragraphs (cont.) Algae are a diverse group of simple plants. They show a diversity of forms, ranging from simple unicells, through colonies and filaments, to complex parenchymatous forms. Being polyphyletic, they also show diversity in their evolutionary lineages. Algae occur in a wide variety of environments, ranging from fresh water to marine and hypersaline habitats, as well as habitats as diverse as swimming pools, polar bear fur, arctic sea ice, and the human body. A diverse assortment of characters is used in their classification. Some of the features used in algal classification have considerable controversy surrounding their acceptability. …

19. Writing Tips: Sentences Writing Tips: Sentences • Sentences should: • Contain no more than one idea • Never stray from the main topic • Not be too long • Be connected and flow logically from one to the other • Not contain “filler” words and unnecessary jargon • Not contain any redundancy • Be properly punctuated • Be grammatically correct

20. Writing Tips: Sentences (cont.) Writing Tips: Sentences (cont.) Examples of “filler” words: • In order to • In the direction of • At the present point in time • A considerable amount of • Accounted for by the fact that • To • Towards • Now • Much • Because The biota exhibited a 100% mortality response to the addition of high levels of the lethal pesticide. High levels of the pesticide killed all organisms.

21. Writing Tips: Words Writing Tips: Words • Words should: • Be essential • Be simple • Have unambiguous meaning • Be spelled correctly

22. Overall process of MS prep.

23. CSE (CBE) Style CSE (CBE) Style • CSE = Council of Science Editors • Reference manual • Provides guidelines on style and formatting for scientific writing • Widely used by authors, publishers and editors working in the biological field

24. CSE Referencing CSE Referencing • In CSE, there are two methods of citing references: • Name-Year (Author-Date) Method • Citation-Sequence (Numbering) Method

25. Name-Year Method Name-Year Method • More common of the two methods • Citations in the text are indicated by placing the author’s surname and the date of publication in parentheses • At the end of the paper, a list is provided in which the full citations appear in alphabetical order by author surname

26. Name-Year: In-text Citations Name-Year: In-text Citations • Surname and year of publication are placed in parentheses, e.g. (Smith 2006) • If the author’s name forms part of the sentence, give only the year, e.g. (2006) • For two authors, separate the names with “and” or “&”, e.g. (Smith and Jones 2004) • For three or more authors, use et al., e.g. (Smith et al. 2005) • When quoting, use quotation marks and give the page number, e.g. (Smith 2006 p 57)

27. Name-Year: In-text Citations (cont.) Name-Year: In-text Citations (cont.) • Multiple references are separated with a semi-colon and ordered chronologically (Smith 1998; Jones 2002) • For multiple works by the same author, give the name once and then separate the years with commas, e.g. (Smith 2000, 2003) • For multiple works by the same author in the same year, use small letters to distinguish them, e.g. (Smith 2006a, 2006b)

28. Name-Year Method (cont.) Name-Year Method (cont.) Example of corresponding reference list: Dal Sasso C & Signore M. 1998. Exceptional soft-tissue preservation in a theropod dinosaur from Italy. Nature 292:383-387. Hecht J. 1998. The deadly dinos that took a dive. New Scientist 158:13. Paul GS. 2000. Dinosaurs of the air: The evolution and loss of flight in dinosaurs and birds. Baltimore: The Johns Hopkins University Press. 472 p. Rogers RR, Krause DW & Rogers KC. 2003. Cannibalism in the Madagascan dinosaur Majungatholus atopus. Nature 422:515-518. Schweitzer MH, Wittmeyer, JL & Horner JR. 2005. Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex. Science 307:1952-1955. Sereno PC, Forster CA, Rogers RR & Monetta AM. 1993. Primitive dinosaur skeleton from Argentina and the early evolution of Dinosauria. Nature 361:64-66.

29. Name-Year Method Name-Year Method Examples of in-text citations: Dinosaurs became extinct 65 million years ago (Paul 2000). A variety of fossil and non-fossil sources provide scientific knowledge about dinosaurs (Dal Sasso & Signore 1998; Schweitzer et al. 2005). The first dinosaurs were “small, bipedal predators” (Sereno et al. 1993, p 64). Hecht (1998) suggests that dinosaurs had to slow down when chasing prey to avoid falling and injuring themselves. It was not until 2003 that cannibalistic behaviour among dinosaurs was confirmed (Rogers et al. 2003).

30. Citation-Sequence Method Citation-Sequence Method • Use superscript numerals to mark in-text citations • Numerals follow the sequence in which you refer to them in the text • A full reference list appears at the end of the paper, numbering references in the same order as they appear in the text, i.e. the reference list is numerical rather than alphabetical • Use the same number if you refer to the same source more than once

31. Citation-Sequence Method Citation-Sequence Method (cont.) Examples of in-text citations: Dinosaurs became extinct 65 million years ago1. A variety of fossil and non-fossil sources provide scientific knowledge about dinosaurs2,3. The first dinosaurs were “small, bipedal predators”4(p 64). Hecht5 suggests that dinosaurs had to slow down when chasing prey to avoid falling and injuring themselves. It was not until 2003 that cannibalistic behaviour among dinosaurs was confirmed6.

32. Citation-Sequence Method (cont) Citation-Sequence Method (cont) Example of corresponding reference list: 1. Paul GS. 2000. Dinosaurs of the air: The evolution and loss of flight in dinosaurs and birds. Baltimore: The Johns Hopkins University Press. 472 p. 2. Dal Sasso C & Signore M. 1998. Exceptional soft-tissue preservation in a theropod dinosaur from Italy. Nature 292:383-387. 3. Schweitzer MH, Wittmeyer, JL & Horner JR. 2005. Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex. Science 307:1952-1955. 4. Sereno PC, Forster CA, Rogers RR & Monetta AM. 1993. Primitive dinosaur skeleton from Argentina and the early evolution of Dinosauria. Nature 361:64-66. 5. Hecht J. 1998. The deadly dinos that took a dive. New Scientist 158:13. 6. Rogers RR, Krause DW & Rogers KC. 2003. Cannibalism in the Madagascan dinosaur Majungatholus atopus. Nature 422:515-518.

33. Reference List Reference List Book: • Author/editor. Year. Title. Edition. Place of publication: Publisher. Number of pages. Book Chapter: • Author. Year. Title of chapter. In: Editor of book, editor. Title of book. Edition. Place of publication: publisher. Pages of selection. Journal Article: • Author. Year. Article title. Journal title volume(issue):pages. Newspaper Article: • Author. Date. Article title. Newspaper title; section:pages(column).

34. Reference List (cont.) Reference List (cont.) Dissertation / Thesis: • Author. Date. Dissertation title [dissertation]. Place of university: Name of University. Number of pages. Conference Paper: • Author. Year. Paper title. In: Editor, editors. Title of volume. Conference Name; Full date; Place of publication: Publisher. Pages of selection. Conference Abstract: • Author. Year. Abstract title [abstract]. In: Conference name; Full date; Place of conference: Title of organization. Pages of selection.

35. Reference List Reference List (cont.) Magazine Article: • Author. Date. Article title. Magazine title:pages. Electronic Journal: • Author. Article title. Journal title [internet]. Year [cited date]; volume(issue):pages. Available from: URL Web Page: • Author. Document title [internet]. Title of complete work; update date [cited date]. Available from: URL • Example from Wikipedia:Wikipedia contributors. Citation [Internet]. Wikipedia, The Free Encyclopedia; 2006 Mar 19, 01:12 UTC [cited 2006 Apr 24]. Available from: http://en.wikipedia.org/w/index.php?title=Citation&oldid=44435410

36. Reference List Reference List (cont.) Format for author names: • Give the surname, followed by the first and middle initials.  • There is no comma following the surname, and no periods or spaces separating the initials, i.e. “Surname AB” • For two to 10 authors, list the authors as above, separating names by a comma and a space • If there are more than 10 authors, list the first 10, followed by “et al.” • If the article is anonymous, write “[Anonymous]” in place of the author

37. Reference List Reference List (cont.) Format for author names (cont.): • If the author is an organization, give the organization’s name here.  If the organization has an abbreviation, put the abbreviation in brackets before its name, e.g. [CBE] Council of Biology Editors  • If there is no author, but an editor or editors instead, list the editor(s) here, followed by “, editor” or “, editors”  

38. Reference List Reference List (cont.) Format for publication date: • For books, book chapters and journal articles, give only the four digit year, e.g. 2006 • If there is more than one work by the same author in the same year, attach “a”, “b”, etc. to the end of the year to distinguish them, e.g. 2006a • For an internet source, give the date the document was published or last updated. Give the year, followed by the month (abbreviated by the first three letters and with no period) and day, e.g. 2006 Apr 25. If the month or day aren't available, omit them • If you're citing an e-mail, give the date the e-mail was sent • For a newspaper article, give the year, followed by the month (abbreviated by the first three letters and with no period) and day, e.g. 2006 Apr 25

39. Reference List Reference List (cont.) Format for publication date (cont.): • For a magazine article: • If the magazine has a date, format the date as you would for a newspaper article, e.g. 2006 Apr 25 • If the magazine is a monthly publication, omit the day, e.g. 2006 Apr • If the date is a season, give the full (unabbreviated) season, e.g. 2006 Autumn • If the date includes a span of months or seasons, separate them by an en-dash (–).  No spaces precede or follow the dash, e.g. 2006 Mar–May • If the magazine has volume and issue numbers (like a journal), you may cite it like a journal

40. Reference List (cont.) Format for title of article or book: • Only the first letter of the first word and proper nouns and adjectives are capitalised • If there is a secondary title or subtitle, it can be included after the main title. Separate the two with a colon • If the work is written in a foreign language, give the title in its original language and follow this with an English translation in square brackets • If the article is an editorial, write “[editorial]” after the title, but before the ending period • If the article is a letter to the editor, write "[letter]" after the title, but before the ending period

41. Reference List Reference List (cont.) Format for title of journal : • All words in the title are capitalised • Title is often written in italics • Unless the title is a single word, most journal titles may be abbreviated according to standard practices • If you are citing a web page that is part of a larger work, give the title of the larger work here • If you are citing an article from an electronic database, give the name of the database here

42. Reference List (cont.) Format for volume and edition (books): • If you are citing a volume with a separate title, write “Volume” followed by the number. Follow the number with a comma and a space and then give the title of the volume as you would the title of the book • If the book is an edition other than the first, give the edition, e.g. “2nd ed.”, “3rd ed.”, etc. • If the book is in the first edition, but later editions are known to exist, specify that it is the “1st ed” • If the edition is given using words, abbreviate it. For example, abbreviate “New revised edition” as “New rev ed”

43. Reference List (cont.) Format for volume and edition (articles): • Give the volume number of the journal • If you choose, the volume number may be followed by the issue number in parentheses. There are no spaces before, after, or within the parentheses • If the article is in a supplement, write “Suppl” after the volume number • If the article is from a newspaper, write “Sect” followed by the section letter or number

44. Reference List (cont.) Format for books (named parts): • If you are citing a specific chapter or other named part, give the name of the part. If it is numbered or lettered, write “Part” or “Chapter” followed by the number and a comma before the name • If the book is a translation, write “Translation of:” followed by the original title • If the book is part of a series, enclose in parentheses the name of the series, followed by a colon and a space, followed by the volume number of this book, e.g. (Series: 2). Also switch the preceding period to a semicolon (;)

45. Reference List (cont.) Format for books (editors and translators): • If the book has an editor(s) (not listed in the author position), list the editor(s) using the name format you would use for an author.  Follow the name(s) with “, editor” or “, editors” • If the book is a translation, list the translator here, using the same format as for an author. Follow the name with “, translator”  • If the book has both an editor and translator, list them in the order they appear on the title page, separating them with a semicolon (;) 

46. Reference List (cont.) Format for books (publishing details): • Give the city of publication followed by the name of the publisher, separated by a colon • If more than one city appears on the title page, give the first city listed • If the city is not well known, the state or country can be given in parentheses after the city name • If the city is foreign, use the English equivalent of its name • If the city cannot be found (after a serious attempt!), write “[place unknown]” • The name of the publisher may be abbreviated • If the publisher cannot be found, write “[publisher unknown]”

47. Reference List (cont.) Format for page numbers (books): • If you are citing the entire book, give the number of pages in the book (counting the index, etc.) followed by “p”, e.g. 256 p • If you only referred to selected pages of the book, or for a chapter within a book, write “p” followed by the page numbers, e.g. p 53–74 • Separate the first and last page numbers with anen-dash • You need only give the least number of necessary digits e.g. 205–7, 205–12, or 295–303 • If the pages are nonconsecutive, list all the page ranges, separating them with a comma and a space, e.g. 12–15, 17-19

48. Reference List (cont.) Format for page numbers (articles): • Include the page numbers of the article • If the article appears on consecutive pages, separate the first and last page numbers with anen-dash • As with books, you need only give the least number of necessary digits • If there are letters as part of the page numbers of journal articles, retain them • If the article is from a newspaper, give the column number directly following the page number in parentheses, e.g. 1(col 5)

49. Reference List (cont.) Format for internet articles: • Write “internet” in square brackets after the title of the article • Give both the web address (URL) and the date it was accessed • If you have to split the URL onto multiple lines, split it only after a slash • Give the publication or update date only after the title of the journal or main website • After the publication or update date, in square brackets write “cited” followed by the date you accessed the page • Format the date as follows: give the year, followed by the month (abbreviated by the first three letters only and with no period) and day, e.g. 2005 Apr 25

50. Other Chapters Next Chapter 1Review of Human Evolution Chapter 2History and Civilization Chapter 3 Philosophy of Science Chapter 4 Weblogs Chapter 5 Scientific Writing & CSE Style Chapter 6 Library Methods Chapter 7 Spreadsheets Chapter 8 Presentations (posters and talks) Chapter 9 Information Society I hope that you found chapter 4 informative, and that you enjoy chapter 5.