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Writing for Scientific Publication
Class Materials

FOR 694

Instructor:  Ruth Yanai, Professor, 176 Baker Lab, tel: 470-6955, e-mail:  rdyanai@syr.edu 

Catalog description of the course:

Three hours of lecture and discussion.  Students will improve their skills in technical reporting by preparing a manuscript suitable for submission to a scientific journal. Topics include selection of an appropriate journal, design of effective figures and tables, sequential preparation of sections of the manuscript, writing tips, peer review, and ethical issues.               

Pre- or co-requisite(s): Students must have research results analyzed and ready to be written up for publication. 

Major concepts or methodologies:

  1. Students will prepare their own research for publication, developing presentation and writing skills.  They will select an appropriate journal, determine authorship, design effective figures and tables, and sequentially prepare sections describing results, methods, introduction, discussion, and conclusions.
  2. Students will review one another's work at two stages, which provides an opportunity to learn about effective writing and constructive review.
  3. At the end of the course, each student's final draft will receive two independent reviews, like those it would receive in peer review through a journal.

Objectives:

After completing this course the student should be able to:

  1. Organize research results and structure them for presentation.
  2. Write at the appropriate level of detail and rigor for the chosen professional audience.
  3. Receive, utilize, and deliver constructive peer review.

Materials:

One or more books on scientific writing will be supplemented by topical readings and examples of papers published in scientific journals.

Recommended textbooks:

Richard J. Gladon, William R. Graves and J. Michael Kelly. 2011. Getting published in the life sciences. Wiley-Blackwell, ISBN-13: 978-1118017166

Josh Schimel. 2011. Writing Science: How to Write Papers That Get Cited and Proposals That Get Funded. Oxford University Press, ISBN-13: 978-0199760244

Until these were published, we used: Day, Robert A. and Barbara Gastel. 2006. How to write and publish a scientific paper. Greenwood.

Grading

Most of your grade depends on your 2 rough drafts (50 points each) and your final draft (100 points).  The 2 peer reviews are 20 points each, and the 2 responses to reviewers are 10 points each.

There are several exercises worth 10 points each.

There are also occasions when you are asked to bring examples or questions; these are 5 points each (probably pass/fail; the main thing is to remember to do it).

Conversion to letter grades will be based on 90 = A, 80 = B, 70 = C, 60 = D, <60 = F.

Rubrics

Outlines

Here's the academic reference on outlines: 

PDF Courtesy of Purdue University, formerly at http://owl.english.purdue.edu/handouts/general/gl_outlin.html

Use an outline to organize your ideas and writing.  

I suggest you adopt this approach (I liked the status report on the sections).  Excerpted from Notes on Writing Papers and Theses, by Ken Lertzman, Simon Frasier University, 

When you first start a writing project, make an outline of the major headings. List the key ideas to be covered under each heading. Organize your thinking and the logic of your arguments at this level, not when you are trying to write complete, grammat ical, and elegant sentences. Separate out the three tasks of: (1) figuring out what you want to say, (2) planning the order and logic of your arguments, and (3) crating the exact language in which you will express your ideas.

Many people find it useful when making an outline to attach page lengths and time lines to each subsection. For instance, section 2.4 may be "Evidence for differential use of canopy gaps by Clethrionomys." To this you might append, '3 more days analysi s, 4 days writing; 10 pages." Such time estimates are usually inaccurate, but the process of establishing them is quite useful. 

It is very easy to write and expand outlines with word processors. When starting a writing project, I create a file in which I first develop an outline as described above. I save a copy of the outline separately and then commence the writing by expanding the outline section-by-section. I usually get ideas for later sections while writing earlier ones and can easily page down and write myself notes under later section headings. This is especially useful for filling out the structure of a Discussion while writing the Results. (For instance, "When discussing the removal experiment, don't forget to contrast Karamozov's 1982 paper-- his Table 3--with the astonishing results in Figure 7.") By the time I get to writing the Discussion, the outline has usually been fleshed out substantially and most of the topic sentences are present in note form.

Here's an outline you might want to start with. 

PDF Courtesy of Craig Jones, formerly posted at http://mri.brechmos.org/wp-content/uploads/2010/01/22/how-to-organize-a-paper/paper_outline.pdf

Here's a template in Microsoft Word, with section headings and some reminders (you'll like using Document Map, if you haven't before)

Authorship Readings

Dickson, J.G., R.N. Conner and K.T. Adair. 1978. Guidelines for Authorship of Scientific Articles. Wildlife Society Bulletin  6(4): 260-261 HTML PDF

Galindo-Leal.   1996.  Ecology 101:  Explicit authorship.  Bulletin of the Ecological Society of America 77:219-220.  HTML PDF

Hunt, R. 1991. Trying an authorship index. Nature 352: 187.  PDF

Primack, R.B.,  J.A. Cigliano, and E.C.M. Parsons. 2014.  Editorial: Coauthors gone bad; how to avoid publishing conflict and a proposed agreement for co-author teams.  Biological Conservation 176:  277-280 HTML PDF

Scheiner, S.M.'s response to A.L. Friend's query "By what criteria should individuals be included or excluded from authorship on a peer-reviewed publication, e.g., journal article?"  posted to Ecolog-L, undated.  PDF

Vancouver Protocol

Authorship Exercise

Presentation of Statistics

PDF

The Submission Process

Each journal has a "Guide to Authors" that outlines the order of sections within a paper, word limits, costs (if any), instructions for preparing tables and figures, and formatting requirements for the literature cited.  You can find these on the journal websites.

You may be prompted for additional information when it comes time to submit—key words, cover letter, article type, suggested reviewers, cover art, and it's unpleasant (and inefficient) to be taken by surprise.

Here are some ppt shows with screenshots of the steps involved in electronic submissions of manuscripts and written summaries provided by students.

  • American Society of Agronomy (ASA) PDF
  • Biogeochemistry PPS
  • Canadian Journal of Forest Research PPS
  • Environmental Science and Technology Summary
  • Forests Summary
  • Forest Ecology and Management  PPS | Summary
  • Journal of Bryology Summary
  • Journal of Forestry  PPS
  • Plant and Soil  PPS
  • Soil Science Society of America Journal Guide for Authors | PPS | Summary
  • Fungal Ecology email (Lesson: Don't accept being dismissed by a machine!)

Webinar for Journal of American Water Resources Association (JAWRA) that covers the submission process for this journal, about 40 minutes in they discuss the peer review process. Link to view recording

Cover letters are often required, which are sometimes quite cursory.  Better cover letters include (especially if requested!) what's new and exciting about this work and why its suited for this journal, and recommended reviewers or why someone might be a particularly poor one.

Author contributions - here are some examples from previous papers. Some journals allow free form and others use CRediT.

Proof and Production Details

Once accepted, you may need to visit the system to review page proofs, assign copyright, answer additional questions, etc.

Ecosphere (Zoom recording)

Environmental and Experimental Botany (slideshow)
Forest Ecology and Management (slideshow)

Mycorrhiza (copy edited PDF)

Ecosystems (Proofing nightmare!)

Examples of electronic page proofs:

Tree Physiology

Biogeochemistry

Ecosystems and corrections list

Ecotoxicology

Global Climate Biology

Int'l Journal of Environmental Analytical Chemistry

Soil Science Society of American Journal

Hydrological Processes Proof and email

Instructions for Reviews

When your manuscript is received by the journal, an associate editor will send it out for review, Here are examples of the instructions provided to reviewers of manuscripts, from a variety of journals. If you study them, you can be aware of what the reviewers will be looking for in your paper. (PDF unless otherwise indicated).

Recommendation: Accept after minor revision etc.

Overall Manuscript Rating (1-100):

Review Blind Comments to Author

Reviewer Confidential Comments to Editor

CONFIDENTIAL Assessment Form:

Short evaluation (1 = Lowest and 3 = Highest)

( ) Originality

( ) Technical Quality

( ) General Interest

Content (1 = Lowest and 3 = Highest)

( ) Introduction presents the problem clearly

( ) Experimental methods are adequate

( ) Discussion adequate and result/conclusions Justified

( ) References are complete and adequate

( ) Keywords + abstract reflect the paper's content

( ) Title clearly reflects paper's content

Presentation (1 = Lowest and 3 = Highest):

( ) The length is commensurate with the paper's content

( ) The English language is acceptable

( ) The quality of figures and table is adequate.

 

screenshot of journal of ecology refree resources

screenshot of journal of ecology paper submission

screenshot of the journal of ecology instructions of reviewers

Sample Reviews

When you write a review, it is important to be fair, professional and not personal in your criticism, and to describe the strengths as well as the weakness of the paper. Specific examples will help the authors and the editors understand your points. Here are some examples of reviews (all PDF):

as well as an article about reviewing:

The case for (more) diversity in peer review. Exploring the history, importance and benefits of being inclusive. 

Want to become a certified peer reviewer? Introducing Researcher Academy's latest free offering - a comprehensive course on becoming a confident referee.

Ten reasons to accept your (next) invitation to review. Why saying -yes-could prove an enriching and rewarding experience in more ways than one.

Rights and Responsibilities of Peer Reviewers.

ACS is working on a video series entitled Publishing Your Research 101. Upcoming episode will address: Responding to reviewer comments and manuscript rejections.

Occasionally, there are funny responses. 

Examples of Responses to Reviews

After you receive a review, unless your paper is rejected, you will be asked to respond to the reviewer's comments. You will need to submit a detailed accounting of your changes (or your reasons for not making making changes suggested by the reviewers) as well as the revised manuscript. Here are some examples of responses to reviewers.

Class Notes

Current or Most recent semester:  Enrolled students should refer to the googledoc (Ruth will provide a link!) for active notes and updates.

Steps to Publication

PowerPoint Slides on steps to publication

Author guide to the publication process (Elsevier)