Peer-reviewed journal articles
Activity # 1: “Peer review”
The following extracts are from The Guide to Publication Policies of the Nature Journals, accessed online at 12 December 2007
Sit the whole class in one large circle. For each of the following sections (1-4), choose a different person (using the lucky-dip cards). For each section, ask the person to readthe extract out loud (pass them the appropriate sheet of paper). That person can then lead the group discussion of the following group discussion question.
1. Peer review
“All contributions submitted to Nature journals that are selected for peer-review are sent to at least one, but usually two or more, independent reviewers, selected by the editors. Authors are welcome to suggest suitable independent reviewers, but these suggestions may not be followed. They may also request that the journal excludes one or two individuals or laboratories. The journal sympathetically considers such exclusion requests and usually honours them, but the editor's decision on the choice of peer-reviewers is final.”
Group discussion question:
Why might journals let authors exclude reviewers?
2. Selecting peer-reviewers
“Reviewer selection is critical to the publication process, and we base our choice on many factors, including expertise, reputation, specific recommendations and our own previous experience of a reviewer's characteristics. For instance, we avoid using people who are slow, careless, or do not provide reasoning for their views, whether harsh or lenient.”
Group discussion question:
If you were on the editorial panel of Nature and received an article submission on “Endophytic actinomycetes enhance wheat growth,” how would you go about finding reviewers for this article?
3. The ideal review should answer the following questions:
“Who will be interested in reading the paper, and why?
What are the main claims of the paper and how significant are they?
Is the paper likely to be one of the five most significant papers published in the discipline this year?
How does the paper stand out from others in its field?
Are the claims novel? If not, which published papers compromise novelty?
Are the claims convincing? If not, what further evidence is needed?
Are there other experiments or work that would strengthen the paper further?
How much would further work improve it, and how difficult would this be? Would it take a long time?
Are the claims appropriately discussed in the context of previous literature?
If the manuscript is unacceptable, is the study sufficiently promising to encourage the authors to resubmit?
If the manuscript is unacceptable but promising, what specific work is needed to make it acceptable?
Is the manuscript clearly written?”
Group discussion question:
Rank the following sources of scientific information from most reliable (1) to least (5)
Another student’s assignment
An article in the journal “Blood”
A biochemistry text book
An article in the “The Advertiser”
An entry in wikipedia
4. “The editors then make a decision based on the reviewers' advice, from among several possibilities:
- Accept, with or without editorial revisions
- Invite the authors to revise their manuscript to address specific concerns before a final decision is reached
- Reject, but indicate to the authors that further work might justify a resubmission
- Reject outright, typically on grounds of specialist interest, lack of novelty, insufficient conceptual advance or major technical and/orinterpretational problems”
Group discussion question:
If you were an author and received a response that “further work might justify a resubmission” but you had no money for the reagents, what might you do?
Activity #2: The parts of a journal article
Journal articles tell a story:
Why you did it/ Why you started/ Background to the issue = Introduction
What you did/ How you did it = Materials & Methods
What happened/ What you found = Results
What it meant/ What you learnt = Discussion
Whose ideas and results your work has used = References
Perform an experiment as a whole class to test the hypothesis that 40% of the students in this class catch the bus to university.
Divide into 4 groups: Assign an article section to each group: Introduction, Materials & Methods, Results, Discussion (don’t worry about References for this exercise). Each group then writes a section of the article for the experiment that was just done. Each section will only be 1-2 sentences.
Join the sections together and read the final article.
Activity #3 Abstracts
Ask someone to read this out:
•The abstract is a condensed version of the entire paper
•The abstract lets the reader decide whether or not to read the paper
•The abstract should be written after the final draft of your paper is complete, even though it is placed at the beginning of the paper
The abstract is similar to the blurb of a novel as it ‘sells’ and summarises the document.
Examples:
The 2003 ABC Quest for The Australian Book That Means Most to Australian Readers:
"Cloudstreet" - Tim Winton
‘From separate catastrophes two rural families flee to the city and find themselves sharing a great, breathing, shuddering joint called Cloudstreet, where they begin their lives again from scratch. For twenty years they roister and rankle, laugh and curse until the roof over their heads becomes a home for their hearts.’
A Structure for Deoxyribose Nucleic Acid
Watson J.D. and Crick F.H.C. Nature171, 737-738 (1953)
‘We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.’
Activity #4: ‘Quiz night’
Keep the class in 4 teams (the facilitators should join teams) and distribute a question sheet to each group(Handout #1).
- Tell the teams to yell out when they have finished.
- Once a team has finished, everyone stops i.e. the first team to finish determines the stop time.
- Ask each group to swap their answer sheet with another group for marking.
- Go through the answers (Answer Sheet– do NOT look at this beforehand).
Handout #1: ‘Quiz night’ question sheet
1. Match the following content to its appropriate section of a scientific paper:
Section / Content1. Abstract / A. A diagrammatic representation of a model that the authors propose based on their results.
2. Introduction / B. The brand name and model of a machine used to collect the raw data for a figure.
3. Materials & Methods / C. A comparison of the results obtained relative to other papers published in this specific research area.
4. Results / D. A summary of research previously published in the specific research area of the paper.
5. Discussion / E. A brief summary of the research presented in this paper, including specific details such as the molecular weights of proteins discovered.
2. Two prestigious journals are ‘Science’ and ‘Nature’. One is American, the other is British. Which one is American?
3. Journals are ranked according to Impact Factor (IF). The impact factor is seen as a measurement of how important the papers published in a journal are. In particular, it measures how much other scientists use that information after it has been published. The equation for determining impact factor is:
IF = the number of times articles in a journal are cited (i.e. put in a reference list of another article) during a year/ the number of articles in the journal that year
Rank these journal from highest (1) to lowest (3) impact factor:
Journal of Cell Biology
Nature Biotechnology
FEBS Letters
4. a) How many Australians have won a Nobel Prize (including all categories)?
b)How many are from Adelaide?
‘Quiz night’ answer sheet
1. Match the following content to its appropriate section of a scientific paper:
Section / Content1. Abstract / E.A brief summary of the research presented in this paper, including specific details such as the molecular weights of proteins discovered.
2. Introduction / D. A summary of research previously published in the specific research area of the paper.
3. Materials & Methods / B. The brand name and model of a machine used to collect the raw data for a figure.
4. Results / A. A diagrammatic representation of a model that the authors propose based on their results.
5. Discussion / C. A comparison of the results obtained relative to other papers published in this specific research area.
2. The two most prestigious journals are ‘Science’ and ‘Nature’. One is American, the other is British. Which one is American?
Science
3. Journals are ranked according to Impact Factor (IF). The impact factor is seen as a measurement of how important the papers published in a journal are. In particular, it measures how much other scientists use that information after it has been published. The equation for determining impact factor is:
IF = the number of times articles in a journal are cited (i.e. put in a reference list of another article) during a year/ the number of articles in the journal that year
Rank these journal from highest (1) to lowest (3) impact factor:
1. Nature Biotechnology (22.672)
2. Journal of Cell Biology (10.152)
3. FEBS Letters (3.324)
4. a) How many Australians have won a Nobel Prize (including all categories)?10: 9 for science or medicine, one for literature
b) How many are from Adelaide?4
Information about the Adelaide Nobel Prize winners if anyone is interested.
Source: Department for Foreign Affairs and Trade. Accessed online at 1 March 2008
William Bragg and Lawrence Bragg
William Bragg and his son Lawrence Bragg—jointly awarded the prize in physics in 1915 for their ‘services in the analysis of crystal structure by means of X-rays’.
Sir William Bragg (1862–1942) was born at Westward, Cumberland, and studied mathematics at TrinityCollege. In 1885, when he was just 23, he was elected to the new Chair of Mathematics and Experimental Physics at the University of Adelaide. In 1909 he returned to England with his wife and Adelaide-born family to take up the position of Cavendish Professor of Physics at Leeds.
Sir Lawrence Bragg (1890–1971) was born in Adelaide and educated at the Collegiate School of St Peter. He topped his final year and won a scholarship to the University of Adelaide, which he entered at the age of15. In 1908 he took first-class honours in mathematics. When the family returned to Britain in 1909 he took up the study of physics at TrinityCollege, Cambridge.
Together, father and son initiated the field of X-ray crystallography. Their work on crystal structure opened a new branch of physics, with particular relevance for biology. Their experiments made it possible for biologists to determine the three-dimensional structure of proteins and to determine exactly how they worked at an atomic level. This knowledge led to the design of drugs tailored to the architecture of the protein at which they are directed.
Howard Florey (Baron Florey of Adelaide)
Howard Florey was born in Adelaide and studied at the Collegiate School of StPeter and the University of Adelaide. After graduating in 1921, he went to Oxford on a Rhodes scholarship to study physiology. After transferring to Cambridge, he earned his PhD in 1927 and MA in 1928. From 1936 to 1962 he was Professor of Pathology at the Sir William Dunn School of Pathology at Oxford.
In 1938, Florey began building on earlier work by British scientist Alexander Fleming on the antibacterial action of a mould, Penicillium notatum. Working with Ernst Chaim, a refugee scientist, Florey investigated the biochemical properties of various antibacterial substances and selected penicillin as the most promising. Florey’s work turned penicillin into a practical drug that subsequently saved millions of lives. Florey, Chaim and Fleming were awarded the Nobel Prize for developing a substance of ‘immediate value to mankind’.
Dr Robin Warren
Professor Barry Marshall (from Perth) and Dr Robin Warren—jointly awarded the prize in physiology or medicine in 2005 ‘for the discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease’.
Robin Warren (1937–) was born in Adelaide, South Australia. He was educated at the Collegiate School of St Peter in Adelaide and studied medicine at the University of Adelaide. After working at the Royal Adelaide and RoyalMelbourneHospitals, he took up a pathology position at the RoyalPerthHospital in Western Australia in 1968.
Together, Warren and Marshall discovered Helicobacter pylori in 1982. They concluded that this bacterium—not stress—causes more than 90 per cent of duodenal ulcers and up to 80 per cent of peptic ulcers. Their work revolutionised the treatment of gastro-duodenal ulcers by enabling an antibiotic cure and has led to a significant reduction in the prevalence of gastric cancer.