writing workshop 2016

© 2016 American Society of Plant Biologists

Tips and Tricks for Effective Writing

University of Nottingham

9 March 2016

Mary Williams @PlantTeaching

[email protected]


How to write papers more effectivelyStructure

The mini articleOutlines and reverse outlines

Paragraph structure: Topic sentences!

Polishing and revising: Use plain language

Ethics of writing

Getting published Read the instructions for authors! Pre- and Post-publication peer reviewEthics of figure preparation


Set aside time for writingDon’t leave it until the last minute


Don’t let good data down through bad writing

“For 90% of submissions, the problem is not the novelty, but the explanation of the novelty”

Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York).

Is your explanation clear enough for a late-night reader?


A good structure is essential: The two-funnel model of a paper

Start broadly: Why is this topic important?

End broadly: Where is this topic heading? What can we expect to come out of it?

Statement of what you did and why

Statement of what you did and why

Methods / Results

Introduction

Discussion


What is the general and specific significance of your work?

www.plantcell.org/cgi/doi/10.1105/tpc.109.tt1009

Title

General Problem(s)

Specific Problem(s)

Unknown

Experiments

Results Description

Figure

Figure Legend

Interpretation

Specific Benefits

General Benefits

Novelty of the new results


The Micro-article

Introduction

Discussion


What is the general and specific significance of your work?

www.plantcell.org/cgi/doi/10.1105/tpc.109.tt1009


The Micro-article

Introduction

Discussion

Handout!


Outlines and reverse outlines can be extremely helpful

Don’t worry about smoothing your writing until you are reasonably happy with the structure

Periodically rename your work-in-progress so you have the option of returning to an earlier version….


Polishing: Use topic sentences- People read in F or E patterns

http://www.jarimbi.com/writing-web-part-1/

Reverse outlining:The first line of each paragraph should be sufficient to convey your meaning

Read just the headings and topic sentences of the handout


(i) Never use a metaphor, simile, or other figure of speech which you are used to seeing in print.

(ii) Never use a long word where a short one will do.

(iii) If it is possible to cut a word out, always cut it out.

(iv) Never use the passive where you can use the active.

(v) Never use a foreign phrase, a scientific word, or a jargon word if you can think of an everyday English equivalent.

(vi) Break any of these rules sooner than say anything outright barbarous.

-George Orwell, "Politics and the English Language," 1946

(i) Never use a metaphor, simile, or other figure of speech which you are used to seeing in print.

(ii) Never use a long word where a short one will do.

(iii) If it is possible to cut a word out, always cut it out.

(iv) Never use the passive where you can use the active.

(v) Never use a foreign phrase, a scientific word, or a jargon word if you can think of an everyday English equivalent.

(vi) Break any of these rules sooner than say anything outright barbarous.

-George Orwell, "Politics and the English Language," 1946

https://www.mtholyoke.edu/acad/intrel/orwell46.htm

Polishing: Use “plain language”

http://www.npr.org/blogs/ombudsman/Politics_and_the_English_Language-1.pdf


Write “simple, declarative sentences”

I am not, indeed, sure whether it is not true to say that the Milton who once seemed not unlike a seventeenth-century Shelley had not become, out of an experience ever more bitter in each year, more alien to the founder of that Jesuit sect which nothing could induce him to tolerate.

I am not, indeed, sure whether it is not true to say that the Milton who once seemed not unlike a seventeenth-century Shelley had not become, out of an experience ever more bitter in each year, more alien to the founder of that Jesuit sect which nothing could induce him to tolerate.

Example of bad writing from Orwell’s essay

What does it mean?


at this point in time now due to the fact that because during the period during has a requirement for needs have the ability to canin a timely manner quickly, promptly in advance of before in regard to about, concerning, on in order to to in the event that if in the near future shortly, soon it has been shown that… no later than June 1 by June 1 pertaining to about until such time as until with reference to about with the exception of except

When possible, use words rather than phrases

In the event that

If


Simple sentence structure: Subject, verb, object is best

Active voice

Passive voice

Yoda voice

Plants need waterS V O

We developed a model S V O

Water is needed by plantsSVO

A model was developed

VO

Water plants need

A model we developed

S VO

S VO


Use strong, meaningful verbs, and avoid nominalization

This sentence provides an illustration of the problems with nominalizations. This sentence illustrates problems with nominalizations. This sentence provides an illustration of the problems with nominalizations. This sentence illustrates problems with nominalizations.

She made the suggestion that we go out to dinnerWe carried out an investigation into the temperature optimumThe collection of samples occurred at the same time each day

Rewrite:

Duke University Graduate School. Scientific Writing Resource. https://cgi.duke.edu/web/sciwriting/index.php

A nominalization is a verb that has been converted into a noun

https://cgi.duke.edu/web/sciwriting/index.php


Duke University Graduate School. Scientific Writing Resource. https://cgi.duke.edu/web/sciwriting/index.php



Use “plain language”

“Please write in a clear, direct, and active style. Write in the active [voice]and use the first person where necessary. Try to avoid long sentences thathave several embedded clauses.”

British Medical Journal

The potentially superior antiplaque and better surface-active properties of amine fluoride and stannous fluoride containing mouth rinses were carefully investigated in a well-designed double blind, crossover study in 10 healthy volunteers.‑

Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer.

Rewrite. Avoid passive voice and unnecessary information


Use “plain language”

“Please write in a clear, direct, and active style. Write in the active [voice]and use the first person where necessary. Try to avoid long sentences thathave several embedded clauses.”

British Medical Journal

The potentially superior antiplaque and better surface-active properties of amine fluoride and stannous fluoride containing mouth rinses were carefully investigated in a well-designed double blind, crossover study in 10 healthy volunteers.‑

We investigated the antiplaque and surface-active properties of mouth rinses containing amine fluoride and stannous fluoride in a double blind, crossover study in 10 healthy volunteers.‑

Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer.


At the end of every sentence ask

Is the point of this sentence completely clear and unambiguous?

Is the key word that carries the theme at the front of the sentence?

Is every word in this sentence adding information?

Can I express any phrases in a single word?Worksheet!


My own writing: Before polishing

Heme is a tetrapyrrole prosthetic group related to chlorophyll; the iron is held in the middle of the ring by conjugation to nitrogen. Heme is a particularly ancient compound that is found in all domains of life and is an essential cofactor for the cytochromes that carry out redox reactions in the electron transport chains present in mitochondria and plastids; heme also is found in peroxidases and catalases. Side branches of the biosynthetic pathway that leads to heme production also give rise to chlorophyll and siroheme, an iron-containing prosthetic group found in nitrite reductase and sulfate reductase. Plants produce and use heme in their plastids but it can also be used in the mitochondria, cytosol and peroxisomes.




Organelles discussed two places




Chlorophyll mentioned two places




Confusing – chlorophyll doesn’t hold iron, heme does


My own writing: After polishing

Heme is an iron-containing tetrapyrrole prosthetic group in which the iron is held in the middle of the ring by conjugation to nitrogen. Side branches of the biosynthetic pathway that leads to heme production also give rise to siroheme, an iron-containing prosthetic group found in nitrite reductase and sulfate reductase, and chlorophyll, in which the tetrapyrrole group is conjugated to Mn. Heme is a particularly ancient compound that is found in all domains of life. Plants produce and use heme in their plastids but it can also be used in the mitochondria, cytosol and peroxisomes. It is an essential cofactor for the cytochromes that carry out redox reactions in the photosynthetic and oxidative electron transport chains and it is found in peroxidases and catalases.

Structure

Related structures & their functions

Pre-eukaryotic origin, made & functions in plastid/ mito


At the end of very paragraph ask

What is this paragraph’s unit of argument?

Is this unit of argument clearly stated in the theme sentence?

Does every subsequent sentence support and provide evidence for the theme sentence? If not, then remove the sentence.


“Does this say exactly what you want it to say in best way possible?”

OMG we’re going to be here all day.....


Just be glad you have don’t have to rewrite by hand / on a typewriter

Roald Dahl (Charlie and the Chocolate Factory,

James and the Giant Peach)

Leonard Cohen (Suzanne, So Long Marianne,

Chelsea Hotel, Hallelujah)


http://aeon.co/magazine/science/what-can-ants-teach-us-about-agriculture/


http://read-able.com/


Ethics of writing

Guideline 1: An ethical writer ALWAYS acknowledges the contributions of others and the source of his/her ideas.

Roig, M. (2014). Avoiding plagiarism, self-plagiarism, and other questionable writing practices: A guide to ethical writing. Office of Research Integrity.

https://ori.hhs.gov/plagiarism-5

https://ori.hhs.gov/avoiding-plagiarism-self-plagiarism-and-other-questionable-writing-practices-guide-ethical-writing



Ethics of writing

Guideline 1: An ethical writer ALWAYS acknowledges the contributions of others and the source of his/her ideas.Guideline 5: Whether we are paraphrasing or summarizing we must always identify the source of the information.







Ethics of writing

Guideline 1: An ethical writer ALWAYS acknowledges the contributions of others and the source of his/her ideas.Guideline 5: Whether we are paraphrasing or summarizing we must always identify the source of the information.Guideline 8: A responsible writer has an ethical responsibility to readers, and to the author/s from whom s/he is borrowing, to respect others’ ideas and words, to credit those from whom we borrow, and whenever possible, to use one’s own words when paraphrasing.








Ethics of writing

Guideline 1: An ethical writer ALWAYS acknowledges the contributions of others and the source of his/her ideas.Guideline 5: Whether we are paraphrasing or summarizing we must always identify the source of the information.Guideline 8: A responsible writer has an ethical responsibility to readers, and to the author/s from whom s/he is borrowing, to respect others’ ideas and words, to credit those from whom we borrow, and whenever possible, to use one’s own words when paraphrasing.Guideline 9: When in doubt as to whether a concept or fact is common knowledge, provide a citation.









Ethics of writing

Guideline 1: An ethical writer ALWAYS acknowledges the contributions of others and the source of his/her ideas.Guideline 5: Whether we are paraphrasing or summarizing we must always identify the source of the information.Guideline 8: A responsible writer has an ethical responsibility to readers, and to the author/s from whom s/he is borrowing, to respect others’ ideas and words, to credit those from whom we borrow, and whenever possible, to use one’s own words when paraphrasing.Guideline 9: When in doubt as to whether a concept or fact is common knowledge, provide a citation.Guideline 12: Because some instances of plagiarism, self-plagiarism, and even some writing practices that might otherwise be acceptable (e.g., extensive paraphrasing or quoting of key elements of a book) can constitute copyright infringement, authors are strongly encouraged to become familiar with basic elements of copyright law.










Ethics of writing

Guideline 17: Generally, when describing others’ work, do not rely on a secondary summary of that work. It is a deceptive practice, reflects poor scholarly standards, and can lead to a flawed description of the work described. Always consult the primary literature.






Ethics of writing

Guideline 17: Generally, when describing others’ work, do not rely on a secondary summary of that work. It is a deceptive practice, reflects poor scholarly standards, and can lead to a flawed description of the work described. Always consult the primary literature.Guideline 23: Authorship determination should be discussed prior to commencing a research collaboration and should be based on established guidelines, such as those of the International Committee of Medical Journal Editors.







Ethics of writing

Guideline 17: Generally, when describing others’ work, do not rely on a secondary summary of that work. It is a deceptive practice, reflects poor scholarly standards, and can lead to a flawed description of the work described. Always consult the primary literature.Guideline 23: Authorship determination should be discussed prior to commencing a research collaboration and should be based on established guidelines, such as those of the International Committee of Medical Journal Editors.Guideline 24: Only those individuals who have made substantive contributions to a project merit authorship in a paper.








http://www.comeon-project.eu/publications/


Read the Instructions for Authors


Which journal should you send your paper to?

Talk to your coauthors



Look at your references



Factors to consider:Reputation, impact factorTime to decisionCost to publishOpen access optionsEditor / editorial boardVisibility (altmetrics)

Homework for the next conference you attend:•Visit each of the publishers in the exhibition area•Find out which journals they publish •Meet the staff (they are likely to be handling your paper soon)•(You might even get a pen!)


Reviews by working scientistsMultiple editors involved in pre-review Rapid turnaround New category: Rapid Report

Most frequently cited plant journal 2014: 73,318


Peer review (classic)

Authors submit to journal

Thanks, but no thanks

Editor evaluates. Suitable?

Maybe

No

Reviewers evaluate. Suitable?

No Author revises

manuscript

Maybe Editor evaluates.

OK?

Yes


ACCEPT!

Reviewers evaluate.

OK?

YesMaybeNot yet

No

What the

world sees


Now / future: Pre-pub peer review, open review, post-pub peer review

Authors submit to journal


Editor evaluates. Suitable?

Maybe

No

Reviewers evaluate. Suitable?

No Author revises

manuscript

MaybeEditor

evaluates. OK?

Yes


ACCEPT!

Reviewers evaluate.

OK?

YesMaybeNot yet

No

Authors put

manuscript on Biorxiv

Open peer review feedback

Post-pub peer review feedback

Pre-pub peer review feedback

What the

world sees


Which system works best for the author?Which system works best for the reviewer?Which system works best for the public?

What are the pros and cons of:Pre- versus post- peer review?

Single blind peer review (author named, not reviewers) versusDouble blind peer review (author and reviewer not named) versusOpen peer review (all named)


F1000Research, PeerJ, EMBO J.

Find a plant paper on F1000Research or PeerJ or EMBO JSkim the reviewer comments and author responsesDo you think being “open” changes the nature of the reviews?

Find a plant paper on F1000Research or PeerJ or EMBO JSkim the reviewer comments and author responsesDo you think being “open” changes the nature of the reviews?

Non-anonymous


has_user_comments[filter]

In search bar include

Non-anonymous


Anonymous


Ethics of figure presentation

Blatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4.

1. Raw image data must be saved and archived intact ….2. Simple adjustments, applied uniformly, to the entire image are generally acceptable …. 3. Cropping and resizing an image is usually acceptable, but both may be construed as

inappropriate …..4. Digital filtering of an image is not encouraged because it can easily mask important

information .…5. Combining images is acceptable only if it is clear to the reader that the images are

from separate sources. It is acceptable to combine the images of two similar gels or two parts of the same gel in one figure, but only if a visible gap is left between the images or the images are separated and each surrounded by a box. It is not acceptable to splice two gel images together so that they appear to be adjacent tracks from a single gel.

6. Selective alteration or processing of one region of an image is not acceptable .…7. When comparing digital images, it is important that they be acquired under identical

conditions …. 8. Image data should be documented both with representative images as well as with

quantitative statistical analysis of sufficient numbers of experiments ….


http://ori.hhs.gov/education/products/RIandImages/guidelines/photoshop_videos/default.html

http://ori.hhs.gov/education/products/RIandImages/guidelines/photoshop_videos/default.html


Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15. http://jcb.rupress.org/content/166/1/11.short

http://jcb.rupress.org/content/166/1/11.short


http://ori.hhs.gov/THELAB http://ori.hhs.gov/rcr-casebook-stories-about-researchers-worth-discussing


http://www.aspb.org/publications/ethics.cfm


Resources and ReferencesGeneral writing resourcesStrunk, W. Jr. (1999).The Elements of Style. http://www.bartleby.com/141/ Guidelines and lessons for good scientific writingCargill, M., and O’Connor, P. (2011). Writing Scientific Research Articles: Strategy and Steps. Wiley. http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1444356216.htmlDoumont, J., ed. (2010). English Communication for Scientists. Cambridge, MA: NPG Education. http://www.nature.com/wls/ebooks/english-communication-for-scientists-14053993/contents (Free ebook - very useful)Duke University Graduate School. Scientific Writing Resource. https://cgi.duke.edu/web/sciwriting/index.php Short, online course for graduate students with examples and worksheetsEditorial (2010). Scientific writing 101. Nat Struct Mol Biol. 17: 139-139. http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.htmlEuropean Association of Science Editors. EASE Toolkit for Authors. http://www.ease.org.uk/publications/ease-toolkit-authorsExplorations of Style. Blog about academic writing by Rachel Cayley.James Cook University. (2015). Academic and Thesis Writing Workshops. Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York). Moreira, A., and Haahtela, T. (2011). How to write a scientific paper--and win the game scientists play! Rev. Port. Pneumol. 17:146-149. doi: 10.1016/j.rppneu.2011.03.007. http://www.elsevier.pt/en/linkresolver/320/how-to-write-scientific-paper-and-win/90020266Nature Scitable Effective Writing. http://www.nature.com/scitable/topicpage/effective-writing-13815989Nature Scitable Scientific Papers. http://www.nature.com/scitable/topicpage/scientific-papers-13815490PhD2Published blogPlaxco, K.W. (2010). The art of writing science. Protein Science 19: 2261 – 2266. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009394/pdf/pro0019-2261.pdfRogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer. http://www.springer.com/medicine/book/978-3-642-39445-4 https://moodle.swarthmore.edu/pluginfile.php/179173/mod_resource/content/1/Good%20versus%20poor%20scientific%20writing%20from%20Silvia%20Rogers.pdfWriting Center University of Wisconsin. (2014) The Writers Handbook: Reverse Outlines. http://writing.wisc.edu/Handbook/ReverseOutlines.html

http://www.nature.com/wls/ebooks/english-communication-for-scientists-14053993/contents


http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.html

http://www.ease.org.uk/publications/ease-toolkit-authors

http://explorationsofstyle.com/

https://egrs.jcu.edu.au/workshops/academic-and-thesis-writing-workshops-series-2-2015

http://www.elsevier.pt/en/linkresolver/320/how-to-write-scientific-paper-and-win/90020266

http://www.nature.com/scitable/topicpage/effective-writing-13815989

http://www.nature.com/scitable/topicpage/scientific-papers-13815490

http://www.phd2published.com/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009394/pdf/pro0019-2261.pdf

http://www.springer.com/medicine/book/978-3-642-39445-4

https://moodle.swarthmore.edu/pluginfile.php/179173/mod_resource/content/1/Good%20versus%20poor%20scientific%20writing%20from%20Silvia%20Rogers.pdf


Resources and ReferencesGuidance from journalsJ Exp Bot: http://www.oxfordjournals.org/our_journals/exbotj/for_authors/Nature: http://www.nature.com/authors/author_resources/how_write.htmlPlant Cell: http://www.plantcell.org/site/misc/ifora.xhtml Figures preparation and ethical issuesBlatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4.Cromey, D.W. (2010). Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics 16: 639–667Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15 Peer Review Guidelines and Policies, Post-publication peer reviewBastian, H. (2014) A Stronger Post-Publication Culture Is Needed for Better Science. PLoS Med 11(12): e1001772. doi:10.1371/journal.pmed.1001772F1000Research: http://blog.f1000research.com/2014/07/08/what-is-post-publication-peer-review/F1000: http://journal.frontiersin.org/Journal/10.3389/fncom.2012.00063/fullMole. (2007). Rebuffs and rebuttals I: how rejected is rejected? J Cell Sci. 120: 1143-1144. http://hwmaint.jcs.biologists.org/cgi/reprint/120/7/1143Nature: http://www.nature.com/authors/policies/peer_review.html Office of Research Integrity. (US Dept of Health and Human Services) The Lab. http://ori.hhs.gov/THELABOffice of Research Integrity. Research Clinic Case Book. http://ori.hhs.gov/rcr-casebook-stories-about-researchers-worth-discussingScience: http://www.sciencemag.org/site/feature/contribinfo/review.xhtmlPLOS ONE: www.plosone.org/static/reviewerGuidelinesProvenzale, J.M. and Stanley, R.J. (2006). A Systematic Guide to Reviewing a Manuscript. J. Nuclear Med.Techn.. 34: 92-99. http://tech.snmjournals.org/content/34/2/92.full.pdf+htmlTimes Higher Education: http://www.timeshighereducation.co.uk/news/can-post-publication-peer-review-endure/2016895.articleReadabilityRavenBlog (2010). Ultimate list of online content readability tests. http://blog.raventools.com/ultimate-list-of-online-content-readability-tests/