Education Program talk:University of Toronto/HMB436H - Medical and Veterinary Mycology (2013 Q3)/Timeline

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Timeline[edit]

I will reserve a portion of the first few lectures to prepare you for your assignment based on the following schedule.

Week 1: Wikipedia essentials[edit]

In class
  • Overview of the course
  • How will Wikipedia be used in the course?
Homework (please complete this by Friday September 20, 2013)
  • Start the online student orientation. During this training, you will create an account (if you do not already have one), make edits in a sandbox, and learn the basic rules of Wikipedia.
  • Once you have a Wikipedia user account, please email me your user name (james.scott@utoronto.ca).

Week 2: Editing basics[edit]

In class
  • Basics of editing
  • Anatomy of Wikipedia articles, what makes a good article, how to distinguish between good and bad articles
  • Tips on finding the best articles to work on your assignments and to contribute to your classmates' assignments.
  • I will provide you with the enrollment token you will need to register for the course by clicking on the Enroll button at the top of this page.
  • Handouts: Using talk pages, Evaluating Wikipedia article quality, Wikimarkup cheatsheet
Homework (please complete this by Friday September 27, 2013)
Milestone
  • All students have Wikipedia user accounts and will be assigned a topic on the course page. All students will also have competed the online training for students (and I will check that you have done it).

Week 3: Final thoughts - citing sources, obeying copyright[edit]

In class
  • We will briefly discuss referencing on Wikipedia and Wikipedia’s copyright policy.
  • I will hand out a topic to each of you that will be the subject of your assignment.
  • Handouts: How to get help
Provisional list of topics (I will assign each student with a topic - you don't get to chose)
Resources

There are a number of excellent online mycology resources you can access to help you with your project. Here are a few:

  • MycoBank - this is an online database that connects you with the most current names of fungi and it provides extensive additional references for many in addition to photographs (so you know what they look like - but remember, you cannot use these photographs in your assignment).
  • University of Alberta Microfungus Collection and Herbarium - This is the world's largest culture collection of biomedically important fungi, and it is located in Canada. The online database contains very detailed records of isolations of fungi from humans and animals, and provides links to the papers where they are documented.
  • Centraalbureau voor Schimmelcultures - this is a very large culture collection of fungi located in The Netherlands. Their website contains a number of searchable databases that provide information on strains of many different species contained in their collection. Lots of these are medically important. The records also provide links to papers where many different aspects of the particular species are described. There are also links to a large number of peer-reviewed publications in the journal Studies in Mycology.
  • Web of Science - This database will help you to locate peer-reviewed papers, including review articles, where you can learn about your fungus. You can access it through the University of Toronto domain through this link, or you can log on through the University of Toronto Library Portal for access. You can search your fungus using its current (and former!) species names in the Topic field. This search will return large numbers of papers (hopefully) which you will need to sort through to find the important ones. Clicking on a paper hyperlink will let you read the abstract, and in many cases, it should provide you a direct link to the full-text paper (again as long as you are logged on through through the university's domain or through the library portal).
  • PubMed is another article search engine which is very useful in searching the biomedical literature. you can access it by following this link. It is not as comprehensive as Web of Knowledge because it is focused mainly on biomedically important topics. But a number of articles can be accessed through PubMed which are absent (or at least hard to find) on Web of Knowledge. PubMed will only provide you links to the full-text of papers that are Open Access.
  • Index Fungorum - This is a search engine similar to MycoBank. Although it is not as comprehensive in some areas, Index Fungorum is still very useful to help you figure out what names your fungus might have had in the past.
  • CMI Descriptions of Pathogenic Fungi and Bacteria – Although many of these profiles are dated (and the names are old), there is still a great deal of useful information in this growing archive. I encourage you to search your fungus (and all of its various historical names) here to see if you find anything worthwhile. Browsing several of these profiles will also give you a clearer idea of how you should approach the writing tone of your article. As long as you are attached to the internet through the University of Toronto backbone, you can follow this link to the CABI portal - Descriptions of Pathogenic Fungi and Bacteria.
  • Doctor Fungus - This is a very helpful website all about medical mycology. Many of the Wikipedia articles that deal with medical fungi cite it, and you will find a great deal of helpful information here. I caution you that the names used on this website may be old or defunct, and so you will always need to check against registries such as MycoBank and Index Fungorum to figure out what things should be called, and also where they belong in the fungal hierarchy.
  • There are a number of great books on medical mycology in the Gerstein Library in the stacks under the call number range in RC117. Also, you may find some worthwhile reference books in the general mycology section at QK603. Besides Gerstein, the Noranda Library at the Earth Sciences Centre has lots of mycology books too. A few that I think are particularly good include:
    • Barron G.L. 1968. The genera of Hyphomycetes from soil. Baltimore: Williams and Wilkins. 364 pp.
    • Domsch K.H., Gams W., Anderson T.H. 1980. Compendium of soil fungi. Vol. 1. London: Academic Press. 859 pp. [embed this reference: <ref name="domsch">{{cite book|last=Domsch|first=K.H.; W. Gams, W.; Andersen, T.-H.|title=Compendium of soil fungi|year=1980|publisher=Academic Press|location=London, UK|isbn=9780122204029|edition=2}}</ref>]
    • Howard D. H. 2002. Pathogenic fungi in humans and animals, 2nd ed. New York: Marcel Dekker. 800 pp.
    • Kirk PM et al. (eds) 2008. Ainsworth & Bisby's Dictionary of the Fungi, 10th ed. Wallingford UK: CABI International. (This is a fungal "encyclopedia" that defines terms & concepts, provides overviews of different taxa and lists important references.)
    • Rippon J.W. 1988. Medical mycology, 3rd ed. Philadelphia: WB Saunders. 797 pp.
    • Samson R.A., Hoekstra E.S., Oorschot C.A.N v. 1984. Introduction to food-borne fungi, 2nd ed. Baarn: Centraalbureau voor Schimmelcultures, Institute of the Royal Netherlands Academy of Arts and Sciences.
    • Watanabe T. 2011. Pictorial atlas of soil and seed fungi, 3rd ed. Boca Raton FL: CRC Press. (The second edition will work if that's all we have.)

Week 4: Develop a bibliography[edit]

Assignment (due Friday October 18, 2013) (worth 5% of your grade)
  • Make sure that your article is created, even if it is a stub.
  • Compile a bibliography of relevant references and post it to the talk page of the article you are working on. Begin reading the sources.
Selecting the right references

As you may have already suspected, all sources are not equal. Some are objective and neutral, based on evidence and analysis; others are subjective and biased, based on opinion and spin. Although this distinction may seem straightforward, it is not always easy to distinguish between the two types of sources. For the purposes of writing an encyclopedia entry on a species of fungus, the very best sort of information is kind that comes from secondary and tertiary sources, based on research findings that were published in peer-reviewed primary sources.

Let me give you an example, and I'll use one that I know a lot about. Say you were writing a Wikipedia article on the fungus, Baudoinia compniacensis. As you can see, there already is an article on this fungus, but let's ignore that for the moment. I described this genus in a paper I wrote in the peer-reviewed journal Mycologia in 2007.[1] It might be tempting to cite this paper to reference a statement such as "Baudoinia compniacensis is a darkly coloured fungus that grows on outdoor surfaces around distillery aging warehouses". Indeed, this is the reference used for a similar statement in the current Wikipedia entry on the fungus. But can we do better? Can we cite something that is a more credible source to support the same few facts, one not from primary literature but rather from secondary or tertiary literature? The core idea here is that "facts" have greater credibility if there is a demonstration that they are "accepted" by more people than simply those who published the original paper. So in the case of Baudoinia, can we find the same facts accepted somewhere by others? One of the sources listed in this entry is an article in Wired Magazine dealing with the fungus.[2] A brief reading of the first few paragraphs of this article reveals the same facts, however in this case, these observations have been verified independently fact-checked by the article's author. Accordingly, the latter is probably a better reference to cite. I would have reservations if, instead of Wired, the article were to have appeared in a source associated with less rigorous journalism, such as online material written by the original authors,[3] or in a publication whose focus was distant from the technical scope of the subject, such as Vogue or Golf Digest. I mention Vogue and Golf Digest as examples here for an important reason - along with Wired, they are all published by the same large US-based publisher, Condé Nast, and as a consequence, they all have the very same journalistic standards and level of fact-checking. But in this case, given the nature of the subject matter, Wired is credible source because it is a science and technology publication. The others would be a stretch. Hopefully you get the picture. Ultimately if you need to use a primary reference to support a fact because there are no alternatives, go ahead and use it, but because of the particular sensitivity of health-related topics, you should only cite secondary sources when it comes to issues related to treatment. For more information I encourage you to read the articles on editing medicine and health topics and identifying reliable sources.

You will notice further down in the Wikipedia article, in the section on Nutrition, the first two sentences are not referenced (they should be!), and the third sentence is referenced to an online website article written by the original authors.[3] As the source of much of the science discussed in the article and the author of the primary references, I am uniquely aware of the potential for bias in my presentation and framing of the facts (Professor Scott is a genius! Such a landmark discovery and a revolutionary finding in fungal biology! An Ig Nobel Prize is surely on the way!). A better reference might be again found in secondary or tertiary sources, in this case perhaps Bernard Dixon's article in Microbe Magazine.[4] Here, Dixon is an independent party who has examined the facts as the original authors presented them, and commented on them objectively. It is for this very same reason that I did not write the original Wikipedia entry on Baudoinia compniacensis myself. Instead, the article was created by User:Rosser1954, an objective third-party whom I don't know but to whom I'm grateful for taking an interest in this very neat fungus!. Indeed, looking around the web, you might find that there is a considerable amount of information about Baudoinia on the website of the company, Sporometrics, Inc.[5] Despite that this information is of very good quality (it was written by Professor Richard Summerbell with whom I co-teach this course), referencing this material on Wikipedia would be suspect because of the commercial nature of the source (see Advertisements masquerading as articles). Full disclosure: I own the company, so again, I can be uniquely critical. For the purposes of scientific Wikipedia articles, you should only consider non-commercial sources (e.g., websites from government, academic, or non-profit entities) unless the referencing of a commercial source supports a fact that is commercial in nature (e.g., it might be appropriate to reference material on the website of Merck & Co. if they had developed a drug based on a natural product derived from the organism in question).

I hope you have gathered by now that writing an encyclopedia entry is quite different from writing a term paper in may ways, one of which is the need to select references carefully to support facts. And although many references may support the same fact, some references are much more suitable than others given the situation.

Week 5: Expand your article in your Wikipedia sandbox[edit]

Assignment (due Friday October 25, 2013) (worth 5% of your grade)
  • Write a 3–4 paragraph summary of your article —with citations— on your Wikipedia sandbox.
Milestone
  • All students have started editing draft articles on their Wikipedia sandboxes.

Week 6: Helping your peers[edit]

Assignment (due Friday November 1, 2013) (worth 5% of your grade)
  • Review and comment on the drafts of at least 2–3 your classmates to help polish their articles and fix any major issues.
  • Leave your comments on their talk page, do not edit their sandbox.
  • Continue research on your article.
Milestone
  • All articles have been reviewed by others. All students have reviewed articles by their several of their classmates.

Week 7: Your midterm exam is this week[edit]

Homework
  • Continue to work on your article

Week 8: Polishing your article[edit]

Homework
  • Continue research on your article.
  • Take a look at several of the articles of your peers and comment on them.

Week 9: Final due date[edit]

Assignment (due Friday November 15, 2013) (worth 15% of your grade)
Milestone
  • Students have finished all their work on Wikipedia that will be considered for grading.

References[edit]

  1. ^ Scott, J. A. (1 July 2007). "Baudoinia, a new genus to accommodate Torula compniacensis". Mycologia. 99 (4): 592–601. doi:10.3852/mycologia.99.4.592.  Unknown parameter |coauthors= ignored (|author= suggested) (help)
  2. ^ Rogers, A. (2011). "The mystery of the Canadian whiskey fungus". Wired. Retrieved 14 September 2013.  Unknown parameter |month= ignored (help)
  3. ^ a b Scott, J. A. "Baudoinia". University of Toronto. Retrieved 14 September 2013. 
  4. ^ Dixon, B. (2009). "The mystery of the warehouse stains (Animacules)" (PDF). Microbe. 4 (3): 104–105. Retrieved 14 September 2013.  Unknown parameter |month= ignored (help)
  5. ^ Summerbell, R. C. "The Distilleries’ Shadow: A summary of knowledge about Baudoinia, the warehouse staining fungus". Sporometrics, Inc. Retrieved 17 September 2013. 

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