Workshop on writing scientific papers (ca. 3 hours) Dr. Brian Metscher

https://ucloud.univie.ac.at/index.php/s/xaEhC7woEPYFzEQ

Workshop on writing scientific papers (ca. 3 hours) Dr. Brian Metscher

The scientific literature

what it is, where it is, what it is for
What are we communicating, and to whom? primary vs. secondary literature

Structure of a scientific paper

Generally what goes in each section
Why this format?
How it reflects the logic of scientific results Flow and unity in a paper

story structure in scientific reports

Some basics for writing papers

Get started! Methods section is easy to start writing. Following the structure of a good paper in your field can help. Composing the first draft:

Sources, summarizing, citing Keep to the main message Write for your audience
Plan to revise

Make paragraphs the unit of composition: one (main) idea per paragraph ...and of communication: each paragraph says something

Sentences:
Tight, clear, and active - exactly who is doing what? Keep related words together
Omit needless words (!)
Make definite, concrete statements
Learn from examples: read aloud

Titles

Abstracts

A basic scheme for abstracts, with examples
Exercise: analyse the content and structure of an abstract from the literature

Figures

Integrating illustrations and figure legends with the main text Tufte books; Rougier, 10 simple rules

Journals and peer review

Print, online, open access submission, peer review, etc.

Purposes of a title Inform, engage, index How to compose a title

keywords => contents and importance

write a title first, and last
Exercise: write a technical title, and a catchy title

Stephen B. Heard, The Scientist’s Guide To Writing: How To Write More Easily and Effectively Throughout Your Scientific Career

Joshua Schimel, Writing Science: How to Write Papers That Get Cited and Proposals That Get Funded

Jan Pechenik, A Short Guide to Writing About Biology, 9th ed. https://1lib.at/book/5005409/e984b0

Strunk and White, The Elements of Style

"What's a journal for?"

https://www.nature.com/articles/d41586-019-01643-3

Wouters et al. Rethinking impact factors: better ways to judge a journal. Nature 569: 621. 30 May 2019

The Non-Scientist’s Guide to Reading and Understanding a Scientific Paper

https://medium.com/elysium-health/how-to-read-a-scientific-paper-695188037080

Short Guide to Writing Abstracts (Metscher)

https://scilitcomm.blogspot.com/2020/03/short-guide-to-writing-abstracts.html

Tufte, Edward, The Visual Display of Quantitative Information https://www.edwardtufte.com/tufte/books_vdqi

Jambor H, et al. (2021). Creating clear and informative image-based figures for scientific publications. Plos Biology 19(3): e3001161. https://doi.org/10.1371/journal.pbio.3001161

Rougier NP, Droettboom M, Bourne PE. (2014). Ten simple rules for better figures. PLoS Comput Biol 10(9): e1003833. https://www.ncbi.nlm.nih.gov/pubmed/25210732

 

 

Short guide to writing abstracts

An abstract must contain the essential elements of the report: it must tell the readers what problem was addressed and the most important results that are being reported. Usually it also indicates something about the importance of the work, such as what it contributes to a long-standing area of research. It may also tell which methods were used, but usually not in detail (unless a new method is part of the report).

A useful formula for constructing abstracts is 1) an opening sentence that indicates what the general area of research is, often as a general statement of an important process or problem; 2) a second sentence that shows where within that area the present report belongs; and 3) something like "Here we present..." or "We have measured/tested...". This is followed by an outline of the main results and then a concluding sentence saying why this is so important.

Here are two examples: 

Covariation between human pelvis shape, stature, and head size alleviates the obstetric dilemma
B. Fischer and P. Mitteroecker 
2015: PNAS 112:5655-5660.
https://www.dropbox.com/s/qos9ked1lp357mu/Fischer15_ObstetricDilemma.pdf?dl=0 

Compared with other primates, childbirth is remarkably difficult in humans because the head of a human neonate is large relative to the birth-relevant dimensions of the maternal pelvis. It seems puzzling that females have not evolved wider pelvises despite the high maternal mortality and morbidity risk connected to child- birth. Despite this seeming lack of change in average pelvic morphology, we show that humans have evolved a complex link between pelvis shape, stature, and head circumference that was not recognized before. The identified covariance patterns contribute to ameliorate the “obstetric dilemma.” Females with a large head, who are likely to give birth to neonates with a large head, possess birth canals that are shaped to better accommodate large-headed neonates. Short females with an increased risk of cephalopelvic mismatch possess a rounder inlet, which is beneficial for obstetrics. We suggest that these covariances have evolved by the strong correlational selection resulting from childbirth. Although males are not subject to obstetric selection, they also show part of these association patterns, indicating a genetic–developmental origin of integration.

On the Origin of Species by Natural and Sexual Selection 
GS van Doorn, P Edelaar, and FJ Weissing 
2009: Science 326:1704-1707.
https://www.dropbox.com/s/6a6uo6yg9mm90ge/vanDoorn09_NatSexSelectn.pdf?dl=0

Ecological speciation is considered an adaptive response to selection for local adaptation. However, besides suitable ecological conditions, the process requires assortative mating to protect the nascent species from homogenization by gene flow. By means of a simple model, we demonstrate that disruptive ecological selection favors the evolution of sexual preferences for ornaments that signal local adaptation. Such preferences induce assortative mating with respect to ecological characters and enhance the strength of disruptive selection. Natural and sexual selection thus work in concert to achieve local adaptation and reproductive isolation, even in the presence of substantial gene flow. The resulting speciation process ensues without the divergence of mating preferences, avoiding problems that have plagued previous models of speciation by sexual selection.

For 18 Mar - Literature searching and article summary

*** No class on 11 March! ***

For 18 March:
 

Searching the scientific literature:

Try using some literature searching tools to locate scientific papers in a field of interest to you.
Bring questions to class!

1) Choose a few keywords in your field of interest, and try searching for articles in at least two different databases - e.g. Pubmed, Web of Science, Scopus, Google Scholar (links below). Try different combinations of keywords, and maybe author names, and see what you find.

2) Choose one article from the lists of results.
Is an abstract available?
Is the full text available online?
Can you find the journal's website easily from the information and links in the database you are using?
How many times has this article been cited by other articles in this database?

Some links:
http://scholar.google.at/
http://www.scopus.com/
http://www.ncbi.nlm.nih.gov/pubmed?db=pubmed
http://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch
These and others are at the UniVie library site - click on "Datenbanken"
http://bibliothek.univie.ac.at/eressourcen.html

Also check out some reference management programs, such as Mendeley, Zotero, EndNote, JabRef, and any others you might know about.

Summarizing a research article:

3) Read this short article on how to read a scientific paper:

https://medium.com/elysium-health/how-to-read-a-scientific-paper-695188037080

Note that this was written for non-scientists, but the ideas (mostly) apply to us as well. We will discuss this article in class. 
(Here is a pdf of the article: https://homepage.univie.ac.at/brian.metscher/Guide_to_Reading_and_Understanding_a_Scientific_Paper.pdf )



4) Read a primary research article in your field or a field of interest to you, and be prepared to give the class a very short oral summary of its main points.

Points to cover (1-2 sentences for each):

What question, problem, or hypothesis does the research address?
What was the approach or method used?
What did the authors find out: what is the most important result reported in this paper?
What is the overall importance or interest of this work?

Please write or print your summary in a form that you can hand in.

Welcome to Scientific Literature and Communication!

300018 SE Scientific Literature and Communication for Biologists

The class will meet on Wednesdays 14:30-16:00 in the Zoology Conference Room.

The first class meeting will be on 4 March 2020.  The Zoology Conference Room is in UZA I, "ground" floor, south end.

If you are on the waiting list, you can probably still get into the course: please attend the first class meeting.

Instructor:
Dr. Brian Metscher
Dept. of Theoretical Biology
brian.metscher@univie.ac.at
http://homepage.univie.ac.at/brian.metscher

This course will guide students through the processes of finding, reading, and understanding scientific papers in English. Students will practice writing and speaking about scientific research in a weekly seminar meeting.

Course activities will include online literature searching, reading scientific papers, understanding the reasoning and logic in a scientific presentation, writing various kinds of research reports, and informal speaking on topics from the literature.

Evaluation is based on attendance and participation (2/3) and completion of homework assignments (1/3). Attendance is required: two absences (excused or unexcused) will be allowed before your grade is affected. 

There will be weekly homework assignments, some of which will include a written assignment to be collected in class; others will include in-class discussion or presentation. These will account for 1/3 of the final mark.

If you are enrolled but cannot attend the first class, you must send me an email about this before the first class. Include your registered name and Matrikelnr.

Some resources for scientific writing

Some Resources for Scientific Writing in English

Where to find relevant scientific literature:

1) The reference lists in recent papers on your topic, especially review articles

2) Colleagues with experience in your field

3) PubMed ( http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed )

4) Web of Science ( http://apps.webofknowledge.com ), Scopus ( http://www.scopus.com/home.url ), available if you are connecting through UniVie

5) Google Scholar ( https://scholar.google.at/ ) is very broad and general, and sometimes links to full-text articles

6) The UniVie Library system ( http://bibliothek.univie.ac.at/eressourcen.html ) includes access to

BIOSIS Previews ( = Biological Abstracts); Zoological Record;

Science Citation Index (also ISI, which includes social sciences and humanities);

ProQuest for doctoral dissertations; Elektronische Zeitschriftenbibliothek (EZB);

and about 1000 other databases

7) Use u:access to get University access to materials online

8) Get a reference manager program you like and start using it

e.g. Zotero (free), Mendeley (free), EndNote (avail. through ZID)

How to learn scientific writing:

1) Read good science writing, and pay attention to how it is presented.

2) Co-author papers with someone who writes well.

3) Practice, practice, practice!

4) Peer-review articles for journals.

5) A Short Guide To Writing About Biology, by J. Pechenik gives helpful advice and examples.

https://1lib.at/s/A%20Short%20Guide%20To%20Writing%20About%20Biology

6) Writing Science, by Josh Schimel (available online through u:search) is very good, and his blog at http://schimelwritingscience.wordpress.com/ is worth a look.

7) Science Research Writing for Non-Native Speakers of English, by Hilary Glasmann-Deal has some helpful lessons (also available online through u:search).

8) The Scientist’s Guide to Writing by S.B. Heard (available through u:search) and his blog at https://scientistseessquirrel.wordpress.com/

9) A helpful guide: https://www.gfdl.noaa.gov/wp-content/uploads/2018/08/Elements_of_Style.pdf

Citing sources and avoiding plagiarism:

Always ask the advice of someone with more experience in scientific writing.

One helpful page is at http://www.northwestern.edu/uacc/plagiar.html

For writing grant proposals:

The Art of Grantsmanship, by Jacob Kraicer http://www.hfsp.org/funding/art-grantsmanship

English language references:

A good English dictionary with usage notes, e.g. Webster's, American Heritage, or one of the Oxford dictionaries, or a good dictionary app

Oxford English Dictionary online: http://www.oed.com; Webster's online: http://www.m-w.com/

Oxford Reference Online, including OED http://www.oxfordreference.com

The essential guide to writing in English is The Elements of Style by W. Strunk & E.B. White.

https://1lib.at/s/the%20elements%20of%20style

The original guide by Strunk, without White's additions, is free at http://www.bartleby.com/141/

All other English style manuals are just extended footnotes to Strunk & White.

German-English (and other languages) translation:

A German-English (or English) dictionary with usage examples: I like the printed dictionaries from Langenscheidt and Harper-Collins, and the Mac OS Dictionary app is good and there are extra plugins for translation dictionaries and other languages.

LEO http://dict.leo.org/ , and Google translate ( https://translate.google.com/ )

For the main European languages, DeepL is new and seems good: https://www.deepl.com/translator