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FOR 694 Writing for Scientific Publication
Class Notes 2014

Class schedule                                



Assignments Due

Jan 13

Why Publish?

Bring your questions

Jan 15

Discuss Getting Started

Getting Started Exercise

Jan 22

Choosing your Journal

Knowing your Journal Exercise

Jan 24

Figures and Tables

n copies of Tables and Figures

Jan 27

Figures and Tables


Jan 29

Outline and Objectives

Two copies of your Outline and Objectives with Abstract (revised)

Feb 3


Draft of Results (two copies)

Feb 5

Materials and Methods

Draft of Methods (two copies)

Feb 10

Writing exercise, in class

Bring a difficult section

Feb 12


Preparation for peer review

Editing and proofreading

Submit Results and Materials and Methods Sections with Abstract and Objectives (for First Peer Review)

Feb 17

Statistical Considerations

Bring your questions

Feb 19


Bring examples from your field, 8 copies, number the paragraphs, staple

Feb 24

Advice, Responses to Reviews

First Peer Review Due
First Reviews.docx 

Feb 26


Bring examples from your field, include Conclusions and Summary if any

Mar 3

Progress on Introductions (shared in class)

2 copies double-spaced

Mar 5

Progress on Discussions

2 copies double-spaced


Mar 10-14 (spring break)


Mar 19

Mid-semester feedback

Anonymous feedback

Mar 19


Submit  Rough Draft and Response to First Reviews

Mar 21

(no class)


Mar 24


Bring examples of RFPs, proposals

Mar 26


Authorship Exercise

Mar 28

Readings on Peer Review


Mar 31



Apr 2

(no class)

Second Peer Review Due

Apr 7

Readings on Publication Productivity


Apr 9


Bring n copies of an example from your field

Apr 14

(no class)


Apr 16

Work session

Sections for review

Apr 21

Abstract review

Title, by-line, key words

Abstracts due

Apr 23

Steps to Publication


Apr 28

Last Class (Final Steps)

Final Draft of Manuscript and Response to Second Reviews


Mon, January 13:  Why Publish?

Why Publish?

Elysa:  To get critical feedback on my ideas, in the peer review process

Quingtao:  So people will know the results of my research, it's a way to communicate with other people

Aditi: Protect my intellectual property.  Get credit for ideas or the work that she has done.

Haiyan:  To meet the requirements of the fellowship.

Yang:  To summarize the results of my two years of hard work.

Brannon:  This is how science advances.  Other scientists will benefit.

Adam:  My results should be used by resource managers. Elysa: Policy makers.

Tony:  The thesis will not be widely read.

Qingtao:  To meet the requirements for graduation

Adam:  Build your resume, competitiveness for jobs

Tony:  To learn how to write a publishable paper

Ruth:  Writing the paper improves my understanding of my work

Adam:  It forces you to review previous work

Brannon:  It's the end product of this process.

Habib:  To survive in academia.

What papers you plan to write

Tony: Tree-soil interaction in northern hardwoods (chemical concentrations)

Adam: Soil nutrient effects on the sweetness of maple sap

Brannon:  Comparison of fine root sampling methods for statistical power

Yang:  Temporal variability of tree nutrients in northern hardwoods

Haiyan:  Effects of forest thinning on soil organic carbon

Aditi: Correleation between chemical structure and shear deactivation of enzymes

Qingtao: Evaluation of ecosystem change in response to acidic deposition using a model

Elysa: Effect of NYS forest viewsheds on residential property values

Habib:  Improving the simulation of acid-neutralizing capacity as a function of dissolved organic carbon

Monica: the relationship of bryophyte biomass to evapotranspiration

What's hard about it?  What do we need to do in this class to help you?

Elysa: My results were not significant.  I can't figure out whether I should collect more data, or figure out how to write my paper without significant results.

Qingtao: Writing is hard.  I don't know how to describe my results, my advisor wants more detail.  I have about ten authors and everyone gives comments.  I don't know how to deal with all these comments.

Aditi:  I have too much information to fit into one paper.  I need to decide which parts are important.

Haiyan: The introduction is hard, because it needs to show what has been done before and how my study will contribute to this literature.  Writing specific objectives is hard.

Yang:  Making a story: I can pick out all the significant results, but not all of them are interesting.

Brannon:  Deciding what citations to use for what points you're making, especially for general points.

You must read the papers that you cite.  You must not cite a paper just because you read the idea there.  Cite the best paper for supporting this idea, given your journal audience.  How to choose?  Quality of the journal.  Accessibility of the journal.  Papers that have been cited a lot might be idea leaders.  But, the fact that other people cite it doesn't mean it's a correct source for the claim (see point A.  Read the paper).  Most relevant.  Most recent might be good because it's likely to reference the earlier material.  Earliest might be good for crediting the original source.  A recent review paper might have all of that.

Three is probably enough.

Brannon:  Selecting a journal.  Suggesting reviewers.  Dealing with feedback from the review process.

Adam:  I have lots of different results, not all that significant, so it's hard to know where to focus the paper.

Tony: How to organize my ideas.  How to interpret the results.  How to express ideas in tables and figures

Haiyan:  My paper was regarded by reviewers as being of local interest.  To publish in an international journal, it needs to have broader appeal.

Habib:  how to organize the paper, what belongs in each section.

Weds, Jan 15: Getting Started Exercise

What did you struggle with?  How can we help you?

Adam:  Picking the main results was the hardest part.  I want to synthesize them more.

Elysa:  How to make the introduction general enough and also specific to my question

Haiyan:  The results:  I found that there wasn't a significant effect.

Aditi:  I couldn't figure out whether some of my statements were results or conclusions

Qingtao: The results keep changing and there are too many to choose from.

Yang: Too many results, not enough meaning.

Tony: I have trouble with the first question, why is this important.

Habib: My statements are similar and maybe they aren't in the right place.

Monica: This is a meta-analysis, and I am still processing the data.

Please revise your Getting Started Exercise and provide it when we review your other materials.  Leave out the instructions and it will read like an abstract!

Wed January 21: Choosing your Journal

Factors to Consider

Adam: Reputation of the journal:  Impact Factor (updated annually)

Yang: Scope of the journal (to match your topic):  look at the journal's statement and at what they publish

Monica:  Breadth of the audience.  For example, the Bryologist is narrower than the J of Bryology, which is more cited in other fields.

Elysa:  I looked at the types of statistical analysis in the articles they publish.  I used a basic statistical model, and some journals want innovative use of statistics.

Tony:  Open Access papers are available to anyone without a personal or library subscription.

Rate of citation is higher for open access papers.

Time to publication: Some journals give this information on their web site.   

Steps to publication:

Submit, AE gets reviewers, sent to review, reviews come back, AE makes a decision, you get it back for revision, revised document might go out for review again, back for decision, copy editing, page proofs, publication.

Qingtao: scope in terms of interest: regional, international, Science or Nature.  Regional journals:  Northern J of Applied Forestry.  Southwestern Midland Naturalist.  

Adam: Audience, practitioners as well as researchers.

Habib:  Length of the article.  Some journals have page length restrictions

Brannon: Acceptance rate

Tree Phys 30%

Time to publication:

J. Env. Manag.  13 weeks from submission to acceptance, 2.5 weeks to appear online, 2.5 weeks for the corrected proofs, 8 for publication

SSSAJ  if they say 3 weeks, I think this is target, not actual

CJFR 8-12 weeks for initial review

Costs of Open Access publication
WRR: $3000 (AGU)

Socioeconomic Planning Sciences: $1800 (Elsevier)

J of Bryology: $254 (Maney)

Forest Ecology and Management: $3300 (Elsevier)

Environmental Management: $2500 (Elsevier)

Tree Physiology: $2800 (Oxford)

PLOS One: $1350 This is an Open Access Journal

Journals you chose

Habib:  Water Resources Research

Elysa:  Socioeconomic Planning Sciences:  interdisciplinary and international. niche.  public sector, society and technical.  Try harder to find the impact factor.

Qingtao:  Environmental Science and Technology, except that my paper is long.

Haiyan:  Forest Ecology and Management (depends on results)

Brannon:  Biogeoscience, papers that inform science and policy decisions.

Monica:  J of Bryology, I cite papers from this journal

Tony: SSSAJ, because it's a soils journal

Yang:  Tree Physiology, scope, including past papers on my topic (variation in methods for tree nutrition)

Adam:  J Environmental Management.  I cite papers in this journal and it reaches practitioners and researchers.

Read the instructions

Abstract:  250 words (WRR, J Bryology, SSSAJ (150 for Notes)

EST:  5000 words (300 words for figures and tables)

FEM:  400 abstract

Tree Phys:  300 abstract.  Separate Results and Discussion.  Conclusions in Discussion.

J Bryology:  20 page limit

1250 characters = 250 words (SSSAJ)

Figures and Tables

Friday:  Elysa, Qingtao, Tony, Habib

Monday: Brannon, Yang, Monica, Adam, Haiyan, Aditi

Color:  check costs for your target journal

Even if you can have color figures, make sure that they are legible in black and white.

Try to get gray scales that are different.  Try line types.  Or use labels.

Axis labels:  Variable (units), check capitalization.

Font size:  make sure that they are legible at the scale they will be printed

Figure captions can be purely descriptive or they can tell us what to think

Consider inset graphs

Maps need a scale, N arrow (esp if not up).  An inset might show us where we are on the planet. Think about readers from other countries when you use political boundaries.

Tables:  It's easier to compare values in columns than rows.  Think about whether to transpose your table.

Numbers in tables should be aligned on the decimal point.

Show SE in parentheses or with a + sign.

Avoid the solidus (/) except to indicate division

Don't introduce new vocabulary, such as acronyms or obscure variable names.

Information in the figure or legend will be read before the figure caption.

Repetition in a table is a sign to look for a better way to organize it.

Digits:  For P values, give to the hundredths place or one significant digit, whichever comes first.

Tell us what error bars mean:  SE, SD, 95% CI

Extreme values:  break the scale, show the number, transform the axis.

Stacked graphs can save space

Make sure you know what types of files you need at the time of submitting your paper (see journal requirements or start a submission)

Titles at the top are good for powerpoint slides.  For your journal article, write a caption.  

Use the same symbols or line types to mean the same thing across your graphs.

If points overlap, consider open symbols

If possible, order the legend to correspond to the graph

Think carefully about putting curves through your data especially if there is no meaning to the model

We would rather read figures and tables right side up.  Check journal format and try not to make things too wide.

Think about what information is useful to your readers.  You might decide to include information that is useful to the authors.

Jan 29: Outline, Objectives

Yang:  I wrote two or three sentences in each section.  It helps me plan my writing.  It's good to organize the story and have the whole paper in mind.  Need help with the structure of the results.

Qingtao:  It helps me not to forget anything.  The introduction needs the most work.

Monica:  It's a good exercise to have a map for writing the document.  Having ideas while writing might not put all the ideas in the right place.  They may need to be moved and combined (and deleted) later.  Discussion and conclusions need review.  Still generating statistical output.

Haiyan:  It was not easy, especially the results and discussion.

Tony:  It helps to think about the big picture.  Discussion and introduction need help.

Elysa:  Since I already wrote the thesis, it was hard to go backwards to the outline.  But my committee has asked for reorganization, and results and discussion get mixed up.  Introduction needs development and the conclusion has results.

Brannon:  I like outlines, we we taught to use them in elementary school.  Feedback on the case for the need for the study.

Adam:  The order of the methods, also the introduction.

Feb 3:  Results

Monica:  I have few results, but the ones I have are statistically strong.  When is it important to report that an expected relationship was not found?

Aditi:  I did a lot of experiments and I have too many results, so it's hard to figure out how to structure them.

Qingtao:  Is the description of my results clear and is it detailed enough?

Yang:  I also have too many results.  I'm not sure whether I should be reporting all of them.  I have multiple elements, tissues, and species.  

Consider electronic archives if your journal offers these.  You could prepare an appendix with all the information in it.

Habib:  I brought a combined results and discussion section, also a results section alone.  I don't know how to begin the discussion without repeating the results.

Adam:  I'm not sure whether I explain enough detail about my results.  It's also hard to know how much attention to give to the non-significant findings.

Tony:  I know how to treat the most interesting results but not what to do with the rest.

Haiyan:  The results are very brief.

Feb 5:  Methods

Adam:  Do they make sense, are they understandable?  Especially the site description.  I don't know how much to cite for lab protocols.

Yang:  Are my sentences understandable?  In what order should I describe methods (some are from the 1980s)?

Order:  Site description (if relevant).  Chronological order is good.  Avoid repetition.

Brannon:  How clear is what I'm doing?

Haiyan:  This part is easy for me.

Tony:  I'm using samples from multiple sources, it's hard to know how to organize them.

Monica:  People told me that sections of my Results, Abstract, and Introduction belonged in the Methods.  Everything I have is Methods!

Habib:  How much detail to include.

Qintao:  I have a figure that belongs partly to methods and partly to results.

Elysa:  I redid my GIS model to include more data.  My results are changing, too.

When should you write out numbers and when should you use numerals?

Write out numbers that are small (less than ten, another rule is 20)

Spell out numbers (chemical symbols, acronyms) at the start of a sentence.

Use numerals when followed by units.

Keep an eye on verb tense.  Past tense should work, can be tricky in site descriptions.

Feb 10:  Writing

Adam:  Not my favorite thing.  Getting started: getting my thoughts in order.  How to start sentences.  Outlining helps.

Yang:  Sometimes I like it and it works well.  Writing is important to taking notes.  Writing in English is hard.  Writing in Chinese is not easy either.

Qingtao:  Writing is not easy.  Scientific writing is different.  Sometimes I get stuck; it's easier if I have strong feelings.

Monica:  It's a very good exercise, when I write in Spanish it's easy to tell people what is in my mind.  It's easy to tell if I have repeated expressions or structures.  I'm disappointed with my writing in English.  

Tony:  I love writing in my own language.  Writing long papers requires more organization than short essays.  I need to practice more.

Haiyan:  When I was a student I wrote papers much faster than now, because I was using English more.  It will help to organize my ideas.  I don't hate writing.

Habib:  Sometimes I love it.  Sometimes I hate it.  When I don't have confidence in what I want to say, I can't write.  Sometimes it takes an hour to write a sentence.  It's not because of the language, I have the same problem in Persian.

Ruth:  You can write a letter to a friend

Monica:  I diagram or paint my ideas with arrows, not with sentences.  Cartoons.

Check out bubble diagrams, this is used to get ideas before starting the outline.

Brannon:  I like reliving the project when I write about it.  It helps me with interpretation.  I always feel self-conscious about the final product.  

Aditi:  Writing helps me organize my thoughts.  I spend too much time selecting the right word.

Fowler's English usage.

Reading helps.  

Smith and Brown

Smith is more concise.  The sentences are shorter.  Paragraph breaks are good.  One idea per sentence.  The subject and verb should be near the beginning of the sentence and should carry the meaning, if possible.

Feb 12: Peer Review

Reviewer Assignments

Monica - Aditi - Habib - Brannon - Qingtao - Haiyan - Tony - Yang - Adam - Elysa - Monica

Review Criteria

Are the figures and tables relevant and necessary?

Is the paper logically organized?

Do the results match the purpose of the work?  (if not, change the question)

Is it easy to read?  Can you make suggestions for improvement?  Grammatical editing is appreciated but not required.

Are the methods sufficiently detailed for a researcher to replicate the study?

Does the content justify the length?

Are the statistical design and analysis appropriate and correct?

Do the methods correspond to the results?

These questions will be more relevant to your next draft

How strong is the reasoning in the Discussion?

Are the conclusions supported by the results?  (Take a look at the abstract)

Is the work original and does it contribute significantly to the field?  We may not be the best reviewers for this question, but you will pick a reviewer who could comment on this later.

Are the references up to date, complete, and appropriate?

Is this paper appropriate to the journal?

Is the title appropriate?

What makes a good review?

Start with a description of the paper, to show that you understood.

Make sure you point out what's good about the paper as well as what needs improvement.

Distinguish general comments from specific comments.  Start with the most general and the most important.

You can give comments that aren't important enough to warrant a response to the editor; you can give edits on the ms that aren't included in your review, or I call them. Comments not worthy of a response

Specific comments are helpful for conveying general suggestions.  Reference the exact place in the paper; line numbers are helpful.

General comments should be carefully organized.  You might use a topic sentence followed by supporting information.

Attention to detail.  

Let the author know if there is anything you don't understand.  

You can annotate the ms. but these comments don't go the AE.  

Be honest.  Be respectful.  Give constructive suggestions.  Try to use positive language. The paper would be easier to understand if it were logically organized.

You might include a summary paragraph, highlighting what's most important.

The review process (for journals)

The reviewers are selected by an Associate Editor.  The reviews are directed to the author.  There is a separate field for comments to the editor.  The reviewers are asked to rate the paper: is it acceptable, does it need revision, should it be rejected.  The AE makes the decision.  

Author updates

Elsya is redoing her methods.  She is presenting her work at a meeting in Watertown tomorrow.  Her draft will be ready Friday.

Tony is ready and happy with his paper.

Qingtao is ready but she is not very happy with it.  See the green areas!

Monica will be ready on Friday.  Needs more development on the results.

Aditi wants suggestions on how to condense the detail, it's very descriptive.

Yang will be ready on Friday.

Haiyan is struggling iwth the results ,will distribute on Friday.

Habib has a version now but will have a better one on Friday.

Adam's is ready.  Are the most important results clear and can you help with the flow.

Brannon's will be ready on Friday.  There are questions about the data sets.

Feb 17: Statistical Considerations

Adam: ANOVA, regression:  ANOVA, Sampling methods

Habib:  regression, histogram, linear mixed model:  ANOVA, Sampling mehtods, regression

Yang:  ANOVE, regression, t-test:  ANOVA, regression

Qingtao:  stepwise regression.  regression.

Aditi: none

Monica: regression.  meta-analysis, sample size test (effect size).  ANOVA, regression

Tony: stepwise regression, cluster analysis, ANOVA, simple linear regression, ANCOVA. ANOVA, Sampling mehtods, regression

Brannon:  power analysis:  in Texas, quantitative methods in geography, multivariate statistics.  currently in regression

Elysa:  regression.  APM 510.

Notes on the approach, from mid-semester feedback:

Getting advice on statistical analyses should be done outside of class.  Keep the class time focused on the presentation issues.  A good way to do this would be to give an example from each student, and get feedback on the presentation.

Feb 19:  Introductions

What needs to be accomplished in an Introduction?

Examples you brought

Feb 24: Reviews, Responses to Reviews

Thoughts on the review process

Elysa:  It wasn't as difficult as I was expecting, given that it's outside my field.

Brannon:  Ditto.

Haiyan:  I reviewed a paper in my field.

Monica:  I wondered if the target journal was so different from what I'm used to.

Qingtao:  I learned something about the topic.

Elysa:  It made me more aware of the gaps in my own paper.

Yang:  I like maple sap.  I suggested subheadings.

Habib:  I read some of the cited papers to help me understand the topic.

Adam:  I wasn't familiar with the topic but that can help identify need for clarity in presentation.  I could make structural recommendations.

Monica:  Writing the report was a good exercise, thinking of the AE as the reader.  How this will improve my own paper.

Missing reviews:  Tony, Yang, Qingtao, Haiyan

How to write a response to reviews

Start by thanking the editor and reviewers.

Address each item and how you addressed the issues.

You might have additional comments for the editor.  If you made important changes that were not requested by a reviewer, describe them for the editor, especially if they are improvements.  You might not mention errors that you corrected that weren't noticed by the reviewers.

Take all the comments seriously.  Your response may go back to the reviewers.

Your goal is to convince the editor that your paper is now publishable.

If the reviewer is wrong, give a good reason why you aren't taking the advice.

If the reviewer misunderstood your paper, fix something to prevent other readers from having the same misunderstanding.

Demonstrate that you made an effort in cases where you don't follow advice.  

You can give citations to support your responses.

Your position should be well supported.  You can admit that you were wrong.

How to distinguish review comments from your responses:  (a) color, (b) Comment and Response, (c) font (italics, plain).  Explain your convention at the top.

Some comments are really trivial. Comments not worthy of a response to the editor

Make sure it's clear whether you made a change.

Try not to be defensive.

You may have to provide information to explain the reviewer's comment. The original text was - You may need to provide quotations from your text.  

It's easier to write the response document as you go, and hard to write it later.  If you need to see changes, you can "compare documents" in Word.

Secret trick:  If you start at the bottom, the line numbers above aren't changing as your revise.

Advice to authors, using anonymous examples

Advice to authors

Data is a plural noun:  Soil nutrient data was provided. Structural data was obtained from a real estate database.

Between two things, among three or more.  "rates were average between three different horizons"

Which and that:  "by selecting the two trees which had the highest average sugar concentration" Which is non-restrictive

TMI:  too much information

Methods sections don't usually include overview statements, so when I read them, I find it alarming that I am not being provided enough information to understand the methods.  It's probably better to omit them.  We built our meta-analysis database based on the information provided by the selected data sources, on climate data series, and on our own calculations.

Throw-away sentences: Dectectable differences between stands of different ages are summarized in Figure 2. The changes in soil properties at depths of 0-20 cm, 20-40 cm, and 40-60 cm after thinning are presented in Tables 2a, 3b, and 2c. The characteristics of the sites are shown from table 1. They don't convey meaning, throw them away.

Give units with values. It may not be important to give the units until you give values.  BS%

Digits:  SOC concentration of 114.52 (14.76).  The mean simulated soil base cations (112.4 + 14.1 ueq/L)

Lots of you have laundry list issues. For sapwood, K had the highest variation in sugar maple, but was the element with lowest variation in yellow birch.  For heartwood, Mg was the element with the least variation in American beech and sugar maple.

Feb 26:  Discussions (examples)

What do you need to accomplish in your Discussion?

Interpretation and explanation of the results

Comparison to results of other studies; what questions remain?  Unexplained results

Other studies related to your results

Limitations of the study or of the approach.

Practical implications

Directions for future study

Complete the story and tie in the results to your original questions


Subheadings, first for results and comparison to other studies.

1-4.  Comparison to other studies

5.  Limitations of this approach

6.  Summary of findings.

Subheading for applications

7-8.  9.  Wanders off, not a strong ending.


1.  Comparison of quantitative results to other studies

2.  Explanations for the results (rejecting temperature)

3.  Reject another explanation (hydrology)

4-5. Possible explanation (changing cation and anion concentration)

6.  Soil solution (vs. stream).  What is unique about this study.

7.  Streams, comparing two data sets, unexplained variation.

8.  Another explanation (microbial activity)

9.  Why this study is important

10.  Implications for environmental recovery.   Ends on a detail, disappointing.


1-5.  Validity of assumptions, one paragraph for each.  Justify by comparison to other data sets.

6-9.  Weathering

6.  Remaining question

7.  Interpretation, unexplained results, implications

8.  deserves future research  mycorrhizal role

9.  Apatite weathering, future research questions

10-20  Implications for management and policy

10-12  Rotation length, leaching, species changes

13-14  spatial variation, landscape scale

15-16  regional scale

17-18  fertilization (forest management)

19-20  policy

Strong ending: leads us to the 22nd century.


This has Results and Discussion combined

1.  Results (regression)

2.  Results

3.  Results

4.  Results of viewshed analysis, relationship to other studies

5.  Relationship to another study, why it's different

6-7.  Conclusions

last paragraph:  Limitations of this study.  Suggestions for future research.


1.  Discussion of results (water stress)

2.  Discussion of results (starch and sugars)

3.  Discussion of results (foliar nutrients)

4.  Discussion of results (leaf area, photosynthesis)

5.  Discussion of results (nitrogen)

6.  Comparison to other studies (nitrogen)

7.  Foliar Ca and Mg, photosynthesis

8.  Leaf area index

Could have had a conclusion or summarize important findings.


1.  Results

2.  Relationship to other studies (depth)

3.  Relationship to other studies (N)

4.  More on N

5-6 Limitations

Subheading 7-9 Results in relation to resource availability

Subheading 10-11 Explanation of results in relation to allocation

Good ending!


Subheadings match the Results.

1.   Comparison to other studies (analytical methods)  This could have gone in the Methods, if it's not important.

2-3.  Comparison to other studies (spatial variation)

4.  Implications for sampling methods

5. Comparison to other studies (temporal variation)

6.  Results

7-12.  Comparison to other studies, explanation of results (long-term change)

8. stand age

9. atmospheric change

10.  soil

11.  mycorrhizae

12.  nutrient ratios

The last sentence refers to the opening problem, but it's vague: deserves further attention. More specific recommendations would have been better.

March 3:  Introductions (yours)

Habib:  For some topics, I wasn't sure whether to put them in the Introduction or Discussion.  Related work could be relevant to both.

Tony:  I'm concerned about leading people to my question.

Qingtao:  Deciding which past works are most significant.

1.  Highly cited work has been influential.  2.  The original work.  3.  A review paper might include both of those.  4.  The one that explains it the best for your audience.  5.  Recent papers cite earlier work.

We don't care where you found an idea.  Give us the best source for us to learn about the idea.  

Aditi:  I thought it was too long, so I shortened it.  Now I wonder if it's sufficient.

Adam:  My lit review of all studies that looked at fertilization and sap sweetness is too long.  It's hard to summarize it.  

Yang:  Are my summaries of previous work too detailed?

Brannon:  My original introduction had questions that weren't answered by my results.  I hope I have a better focus now.

Haiyan:  I couldn't answer the question, the Introduction probably needs to be modified.

Elysa:  I think mine is still too long, some of this might go to the Discussion.  I started taking things out and then putting them back in again.

March 5: Discussions (yours)

Yang:  My results changed, so my Discussion isn't finished yet.

Elysa:  Trying to condense it, select the most important topics for discussion.  One of the more significant results wasn't emphasized in my original introduction, maybe I'll change that.  4 pp.

Tony:  How to discuss insignificant results?

The Getting Started Exercise can help you focus on what's important.

Haiyan:  I am still revising the Results.  I brought a different paper, I'm revising it after review.

Monica:  I am revising the Results (adding more studies).  Reviewing the Introduction on Monday helped me strengthen the paper.  I don't have a Discussion yet.

Qingtao:  I don't explain the results enough; I don't have much to say.

Topics for discussion:  What questions remain open?  Comparison to other studies.  Practical implications.  Shortcomings or problems with the methods.  Alternatives to this approach.

Brannon:  Some results have changed, and my Discussion was mostly results.  I've started it, I'm worried about not having enough.  

Adam:  I'm happy to have a draft of the whole paper, but I'm not happy with the Discussion.  It's choppy, content needs review.

Habib: It's difficult to transition between discussion of the different results.  Monica: the larger context.  Brannon: Use sentence structures that refer to the results rather than stating them.

Aditi: I tried to separate Results from Discussion and it wasn't easy.

March 18:  Feedback for Improvement

1.  Below is a list of the topics and activities in the course so far.  Please indicate which you found especially useful, which least useful.  (Scale of 1 to 5 with 5 being most useful.)  Give specific suggestions for improvement if you have any.

Why Publish?  

Getting Started  

Choosing your Journal  .

Figures and Tables .

Outline and Objectives


Materials and Methods

Writing exercise, in class  

Preparation for peer review

Introductions (examples)  

Discussions (examples)

Statistical Considerations  

Responses to Reviews  

Progress on Introductions (yours)  

Progress on Discussions (yours)  

2.  What future sessions would most help you prepare your manuscript for publication?  Are there other related topics you would like to address that aren't on the list?  Here are the proposed future topics, please rate them on a scale of 1 to 5.

3/22:  Readings on Peer Review        

3/24:  Ethics  

3/26:  Authorship  

3/311:  Proposals

4/2:  Readings on Publication Productivity

4/7:  Reviewer feedback and help session  

4/9:  Writing exercise, in class  

4/14:  Abstracts (examples)

4/16:  Work session  

4/21:  Abstracts (yours)  

4/23:  Steps to Publication  

4/28:  Last Class (Final Steps)  

3.  There are many ways we can work together.  Do you have comments or suggestions on the value of these alternatives?

Pairs or triples, trading feedback in class

Writing formal reviews out of class

Informal peer assistance outside of class

Group discussion

Going around the table to equalize participation

Class notes


4.  We have a very diverse group of papers, and we don't all know each other's fields.  Do you have any suggestions for improving our effectiveness in spite of this diversity?  How much diversity is desirable?

5.  Other comments or suggestions..

March 22:  Second Draft

Reviewer assignments

You will review the paper of the person after you in this list:  Elysa - Aditi - Haiyan - Yang - Habib - Monica - Qingtao - Tony - Adam - Brannon - Elysa

March 24: Ethics

Outlier: 139 (Yang, Qingtao)

Yang, Qingtao:  Normally, you check for errors and remeasure if necessary.  There is a statistical definition of outliers (these are not).  Some data entry errors can be recognized as impossibilities.

You can analyze the data with and without the outliers and report both.  This could be an advantage.

Conflicts of interest: 142, 144  (Elysa, Tony)

The first example involves competing biotechnology firms.  It's safest to publish and establish credit that way.

Monica:  We had an arrangement with Chiquita Banana, and we negotiated the right to publish, at the expense of some of their funding.

The second example involves patents.  This is not good for a graduate student who wants papers to be submitted as soon as possible.

Problems like this may become more common with reductions in public funding.

Who else can a student talk to?  Other committee members.  Grad Coordinator.  Dept Head.  Office of Instruction and Graduate Studies.

It's never too early to discuss intellectual property.  Plans for publication.

Allocation of credit: 145  (Adam, Haiyan)

Ben made a presentation about his techniques at a conference.  Another researcher asked him about it and then beat him to publication.  This researcher could have brought him in as an author or at least cited the presentation.  Could Ben's advisor have protected him from this outcome.

Being generous has benefits in building collaborations, if people don't take advantage of you (which is rare in some fields).

Authorship (credit): 146,147, (Monica, Habib)

What credit should be given Jocelyn Bell for the discovery of pulsars?  Her advisor got the Nobel prize.  She was an author of the paper.

The second case is a conflict between a junior professor and her students over how to divide their results among papers.  It's better for the students to each have their own paper; it's better for the professor to write a single comprehensive paper.

Again, this should have been discussed in advance: the plans for publications and the authorship.

Advisors should be credited for papers in which students are lead authors.  They can be flagged in a listing of publications.

Misconduct:  148, 149, 150 (Brannon)

A student notices that another student is fabricating data but is afraid to offend the advisor.  Collecting evidence would be good.

In a grant proposal, a student cites a paper as submitted that wasn't submitted yet.  In preparation is what he should have said.  Unpublished data is what journals will use for a paper that hasn't been accepted yet.

Franklin told the story of the imaginary mushrooms described by Lloyd when he wanted to make fun of the new methods.

Alex told a story about the criteria for inclusion in a breast cancer study--it was supposed to be only 30 days between diagnosis and treatment.  Alex's dad would change the date to allow patients to participate; he didn't think it was important to the outcomes.  

March 26:  Authorship

Elysa:  Smigielski, Bryant, Bevilacqua, Wagner, Kuehn.  The exercise helped order some of the minor authors.  

Brannon:  Barr, Yanai, Fahey. Point system delivered as expected.  

Fahey collected the data but hasn't been involved with the paper yet.  Identifying your authors early means that you can ask them earlier to help with your paper.

Provision of unpublished data often warrants authorship.  Do the point systems allow authorship for contributing only in the data area?  Monica pointed out that data collection involves planning.

Brannon offered authorship to a researcher who provided data, who requested acknowledgement instead.  Some authors will not be involved in the production of the paper.

Monica:  Berdugo, Dovciak, Kimmerer.  The point system agreed with the order I expected. 

Tony:  Dong, Yanai, Briggs, Johnston, Fisk, Acker, Vadeboncoeur, Schirmer.  

100, 70, 55, 45, 25, 10, 15, 20.  

Schirmer:  Sample analysis is usually compensated monetarily.  When you don't have money, you can ask people to contribute work to your paper by offering them authorship.

Acker provided data on soils and litter chemistry.  These data have already been published.  Ruth will check correspondence with Acker and Arthur about their involvement.

25 points is the threshold for inclusion, do you disagree with that? 

Yang: Yang, Yanai, Lily, Fatemi, Briggs.  90, 50, 40, 40, 40.  

Fatemi and Briggs contributed unpublished data.  Paul has been involved in creating the paper.  

Is the last author a position of honor or is this the person who contributed the least?

Monica was a middle author on a paper with Europeans where the last author was the leader of the project.  The people who wrote the paper were first.

Ruth has a collaborator in Korea who prefers to be last and corresponding.

In China, the corresponding author counts, regardless of the position.

Habib:  Fakhraei and Driscoll

Habib would have given more weight to the writing.  Should the person who writes the paper always be first?

Ruth's first post-doc paper had as first author the leader of the group, who hadn't published.

Habib hadn't published his masters, someone offered to help with writing who hadn't been involved.

When multiple papers are involved, authorship should be fairly distributed across the collection.

The categories in the point system mean different things in different types of studies.

Adam:  Wild 100, Yanai 20.

What about funding?  Does the person who wrote the grant get authorship?

Monica contributed stemflow and throughfall data to a project in Columbia (design and sample collection) but the collaborator who analyzed the samples is not sharing the data or involving her in the writing.

It's helpful to discuss in advance the plans for authorship and other aspects of intellectual property.

Choosing collaborators is also important.

Consult the Montreal Protocol for a definition of authorship.

  1. Use the point system described by Carlos Galindo-Leal in Ecology 101 (Bulletin of the Ecological Society of America, October 1996).  Make a column for each of the possible authors of your paper, and assign points for your various contributions.  Include yourself! - Planning, Executing, Analyzing, Interpreting, Writing 
  2. Do the five categories of contributions suggested by Galindo-Leal seem appropriate for your project?  If you prefer, try applying a point system with different categories, such as those suggested by Hunt or Dickson and Conner.
  3. Name your authors, in the order you propose to list them on your publication.
  4. Does your list agree with any objective point system? If not, what were the other factors that influenced your decision?
  5. Who will you list in your Acknowledgements section?

Author lists


March 24: Proposals

What's in a proposal

Abstract or Summary: focuses on the problem, there are no results.  There may be required sections (e.g. NSF Summary, with broader impacts)

Background and Justification, Rationale and Significance, Introduction, possibly requireed in some order relative to the Objectives.

There may be a section for Progress Report, in a renewal proposal.  NSF requires a section on Prior Support.

How early are the Objectives?  Depends on the required format.

Approach, Experimental Plan, Research Methods: may be less detailed than in a paper.  They need to be convinced that you know what you're doing but not enough for another researcher to replicate the methods.  Methods  will be in future tense in a proposal but past tense in your journal article.  

Verb tense: We will or If funded, we would  Future tense is simpler.  We expect (present tense).

There will be strict length restrictions on proposals.  15 pp for NSF, 14 USDA, 5 pp for a pre-proposal.  Tricks for squeezing your proposal: font, heading format, formatting of figures and tables.  Use all the space.  Reviewers will always wish that you had explained more.

Objectives and Hypotheses:  This is more important than in a paper.  You may have an overall goal in addition to specific objectives, hypotheses, alternative hypotheses.  There may be sections to the Objectives, corresponding to sections of the Methods.  Hypotheses may be important to the Methods section.

It's important to show that the proposed activities will achieve the objectives.  

If you end the Methods with Data Analysis and Interpretation, you can show how your hypotheses will be tested or objectives achieved.

Endings: Outcomes, dissemination of results.

Timeline or Schedule: Might be a required section.

Personnel:  Might be under approach, Budget Justification, or Organizational Plan

Supporting letters:  Showing that the people have agreed to provide data, sites, facilities, instruments.

Budgets and Budget Justification, may be limited to one page.  This is a place where you can convince reviewers that you have thought through your project.  Point out where costs can be saved by using existing data or collaborating with other projects.

Asking for too much money can reduce your chances of getting funded.  How do you find out how much to ask for?  You can look at past funding records.  Consider what you actually need.  

Conflict of Interest:  These people cannot be asked to review your proposal.  Conflicts include family members, co-authors or collaborators or other financial interests (might be 4 or 5 year time limit), anyone at your institution, major professors, student advisees.

Current and Pending Support:  Is the time available for the participants to commit to the project.

April 2:  Peer Review (Readings)

Nepotism and Sexism in Peer Review (Monica)

Correlation analysis of Swedish peer review of 114 grant proposals, women's proposals had lower ratings for the same productivity (using 6 metrics based on publications).  The status of the institution also affects the ratings.

Gender Bias in the Refereeing Process (Elysa) 2002

2680 manuscripts, they didn't find a bias between acceptance rates for men and women.  There may have been a bias in the editors that agreed to participate in the study.

There was a bias by country, even controlling for wealth. 76% of papers were from non English-speaking countries, acceptance rate of 41% vs. 33%.

When Peer Review Fails:  Problems with a Giant Lasar Project (Brannon)

Lawrence Livermore Lab was building an expensive lasar project, with review panels stacked with people involved in the project.  They were covering up the fact that there were unsolved problems and that the project wasn't ready for construction.

Recommendations to Congress to prevent further occurrences.

Effects of Blinding on the Quality of Peer Review (Aditi)

127 manuscripts assigned to two reviewers, randomly assigned to blind treatment (remove the authors names and credentials), score the quality of the reviews.  The quality of reviews: attention to the importance of the questions, target key areas, strengths and weaknesses, constructive comments on quality of the presentation and writing.  Quality was higher when blinded.  The authors and AEs also rated the blinded articles as better.  If the reviewers were asked to sign their reviews, the reviews didn't score higher, but the authors noted that they were nicer (more courteous, constructive, and more fair).

The Effect on the Quality of Peer Review of Blinding Reviewers and Signing the Reviews (Haiyan)

420 reviewers from a database, 221 agreed to review a paper that was already accepted for publication.  They found no effect of blinding on the rate of detection of errors.  They introduced 8 errors of design, analysis, and interpretation. 

A Troubled Tradition (Habib)

Double-blind review (the author is unknown as well as the reviewer), 12% bias associated with the prestige of the institution.  Bias towards submissions from the US, based on the comparison of blinded and unblinded reviewers.  

A Korean scientist published a paper in Science on stem-cell research, the results were not justified by the data.  The papers were retracted.

Drawbacks of Peer Review (Yang)

The fate of a paper depends on who it gets for reviewers.  They sent one paper to 45 reviewers (all on the editorial board), giving them 8 criteria to rate (scientific merit, clarity, statistics, methods, references, tables and figures, discussion, writing) on a numeric scale.  Ratings spread over the whole range.

Plagiarism Charge Casts a Shadow on Peer Review (Tony)

David Bridges declined to review another author's paper (after reading it) saying that he was working in a similar field, and rushed to publish it.  NIH investigated the case, the experimental materials were shipped after the date that he declined the review.  The paper was retracted.

Philosophical Basis of Peer Review and the Suppression of Innovation (Qingtao)

Innovative work may have difficulty passing peer review, which is inherently conservative.  For example, Rous received the Nobel Prize only 60 years after the original innovation.

Peer Review Practices of Psychological Journals:  The Fate of Published Articles Submitted Again (Elysa)

12 recently published articles were submitted to the same journals in which they had been published.  Only 3 were recognized as having been previously published.  Of the other 9, 8 were rejected.

Commentary on this paper by a physicist:  It's harder to evaluate articles in the field of psychology.

A Case for Instant Peer Review (Habib)

Previously, peer review occurred after publication. Now we publish only what we all agree on, which hinders the progress of science.

April 7: Publication Productivity (readings)

Gender, Household Labor, Scholarly Productivity,  (Elysa)

A questionnaire was sent to married faculty (37% of the respondents were women) at a large public university in the southeastern US in 2001.  How many hours per day they spend on research, teaching, service.  Women spent 43% more time on household labor.  Men spent more time on research and women spent more time teaching, even accounting for ladder positions on the tenure track.

Changing Patterns of Publication Productivity (Adam)

A survey of faculty at universities, 5300 respondents from 301 colleges and universities. Pressure to publish. Publication rates are increasing, even at 2-year colleges and liberal arts colleges.  Articles count more than books.

Gender, Family Characteristics, and Publication Productivity among Scientist (Qingtao)

1215 full-time tenure-track faculty responded to a survey.  Women in subsequent marriages are more productive than women in first marriages (because they are more likely to be married to another scientist, which is good for productivity).  Women with pre-school children are more productive than women without children.  Women with school-age children are less productive.

Motherhood and Scientific Productivity (Elysa)

Women with children were more productive than unmarried women or married women without children.  Men's productivity is not affected by having children (in Norway).  1979-1981.

Childcare, Research Collaboration, and Gender Differences in Scientific Productivity (Haiyan)

Same lead author, in Norway, surveyed 1529 scientists, 1989-1991.  After age 10, children don't affect productivity.  Women are more affected by child care.  Women with young children lack research collaboration, which affects their productivity.

Publication Productivity among Scientists: A Critical Review (Tony)

Productivity varies enormously among scientists.

Individual characteristics:  Age: the greatest productivity is in the late 30s and early 40s.  Personality type.  High ego strength, impulse control, care for precision and exactness, preoccupation with ideas.  Childhood experience (autonomy, independence, and self-sufficiency).

Institutional characteristics:  The quality of the education matters, but the quality of the employing institution matters more.

Cumulative advantage and reinforcement of these factors.

Towards a Pluralistic Animal Science Post-Liberal Feminist Perspective (Monica)

Male society values aggression, dominance, and competition.  Characteristics associated with females (nurturing, communicating, cooperation) are not as valued.  The post-liberal feminist perspective sees us a products of all the relationships in society.  How could the feminine values be included in the evaluation of faculty success?

Publish or Perish?  A limited author analysis of ICA and NCA journals (Brannon)

They analyzed the author status of 8 communication journals over a 5-year span.  Full Professors are more productive, there was not a difference between Assistant and Associate professors.  Men published more because there were more in the senior ranks.  Female graduate students were publishing more, male Assistant Professors were publishing more. 

Publish or Perish?  Some Reasons for Perishing (Habib)

Five reasons that people don't publish.

1.  They think it's not worthy.

2.  They are too busy.

3.  They are too critical of their own work.

4.  They can't tolerate criticism from others.

5.  They can't organize the data into a publishable format.  They can't distinguish what's important and omit what is not.

Recommends Day's book, How to Write and Publish a Scientific Paper.

If you don't publish it, your research hasn't been done.

Equity and Equality in Measuring Faculty Productivity (Yang)

Faculty survey of publication productivity.  There is no difference between men and women publishing fewer than 50 paper.  But fewer women publish more than 50 papers (0.7% of women, 6% of men).  Of faculty who don't publish:  43% of women, 23% of men.  (Is the response rate higher for women in this category?)  Women are more likely to be junior authors and to publish on non-mainstream topics.  They are more likely to write books.

Feedback with Anonymous Examples

Write about your subject area, cite the statistics.  Instead of there is a negative correlation between annual temperature and understory moss cover, say understory moss cover is higher in cooler climates. Instead of - In both models, square footage, number of bathrooms, the year the structure was built - yielded positive and significant results, say, Bigger houses, newer houses, and houses with more bathrooms sold for higher prices.

Look at subjects and verbs of sentences. It can be said.This shows It suggests - do not carry the meaning of your sentence.

Throw-away sentences:  Describe your results, not your tables and figures. Detectable differences for ANOA within stands of samples sizes up to 50 are summarized in Figure 1. The results from the GIS and statistical analysis are presented in Tables 2 and 3.

fewer is used with count nouns, less with mass nouns. enzymatic reactions produce a very high yield with less byproducts.

Don't start a sentence with a numeral or abbreviation.  1 unit of an enzyme is defined as - 5 samples were collected from each plot. PVC cores were collected by Tim Fahey. What about pH?

April 9 Abstracts (examples)

Bring at least one abstract for us to review.  4 copies is enough, if we share.  

Progress reports

Adam defended yesterday and will be redoing the statistics.

Yang is still on the second draft; his data set doubled, and he's improving his literature review.

Brannon has a mountain of revisions to make and will be doing statistics on his statistics.

Qingtao's paper is 7000 words but the journal limit is 5000 words.  She will give it to her co-author at the end of the week.  She is using a tutor at the SU Writing Center.  She found that there is also a Graduate Writing Program, where you meet with an editor, and a Graduate Editing Program, where you can send your thesis (with approval of your advisor).

Haiyan is still revising results, reducing the data on soils but adding information on aboveground composition.  Describe how you choose which date to report.

Monica added to her results between the first and second draft.  Most of her studies are in North America.  There are just a few from Asia, Scandinavia, and South America.  So she is considering whether to restrict her analyses to North America.

Tony is revising the paper, and he has an appointment today with the Writing Center.  One more review before distributing the thesis.

Elysa has a lot of revisions, she's also preparing the thesis.  Consider manuscript format.

Analysis of Abstracts


1.  Motivation, importance, problem to be solved.


1-2 Methods.  3-5 Results. The sample-size requirements are given for each element at the selected level of accuracy.  Weak ending.


1 Methods.  The rest are results or interpretation.


1-2 Problem statement.  An alternative explanation is their product.

Weak ending, stronger in the paper.


1.  Problem statement, but it doesn't say why it's important.  not well known is not good enough.

2.  Objective

3-4.  Methods

5-7. Results

8-9.  Conclusions

Endings:  More information is needed


1.  Knowledge gap.  (doesn't say why it's important)

2.  Objective.

3.  Methods

4-5.  Results.

6.  Conclusion, draws attention to the novelty of the results:  have not been previously demonstrated)

7.  Recommendation.  Good ending!


1-2.  Background, problem statement

3.  Knowledge gap and why this is important.

4.  Objectives.

5.  Methods

6-7.  Results

8.  Interpretation

9.  Result

10-11.  Interpretation

12.  Importance, direction to future study, implications for management (over centuries!)

Elysa's worst case

1-2.  Methods

3.  Results

4.  Conclusion is good, suggests what the problem statement should have been.

Elysa's middle case

1.  Importance.

2.  Objectives.  The aim of this study

3.  Methods

4-5.  Results.

Elysa's best case

1.  Problem statement (existing literature is wrong)

2.  Objective

3.  Scope (What they did, sometimes this is what we get for objectives)

4.  Results

5.  Interpretation

6.  Implications.  Different topic from the one in the problem statement.

Literature citation

Format:  Check instructions to authors.

Fonts, use of italics.

Order of initials relative to surname, periods after initials, commas.

Year in parentheses.

Order of listing.  Number systems are difficult to do correctly by hand.

Formats for books, chapters, proceedings, web sites, databases.

Software:  Zotero, Endnote, Mendeley

This will save time and prevent errors in formatting your citations

Monica likes Mendeley because she can read, take notes, and tack places to refer to again.

Brannon and Qingtal use Zotero, which is free.  It helps you organize your pdfs and link them to your biblographies.  You need the stand-alone for it to work off line.  It works well with Firefox.

Why cite the literature?  To help the reader, to give credit, to establish credibility

Monica:  Some journals have a section for a bibliography, in addition to literature cited.

Do not include articles in preparation, personal communications, or unpublished results.  For your own work, you can say, data not shown.


How many are you allowed?  Check instructions.

Don't include words already in your title.

What keywords will your readers use?  Check relevant papers.

Author affiliations: have these ready.

April 14: No class

You could decide to meet for a work session if you want.

April 16:  Help with Revisions

Status: How's it going?

Qingtao:  Overall structure of the paper.

Monica:  She is working on figures, including the map.  

Habib:  He is working on sentence structure and deleting sentences that are less relevant.

Adam brought methods (results are changing), some areas might need more explanation.

Elysa:  Results are final.  Discussion and conclusion is what she is working on now.  She also has a statistical question.

Tony:  Discussion, check for coherence and depth.

Brannon needs to read and add references.  He will also be adding data to the analysis.

Yang:  He is waiting for confirmation of the statistical approach, then he can finish the results.  He brought the Introduction, check structure and content.

People who want another review:

Habib: review for focus (identify material not related to his topic) and sentence structure.

Monica will want review after she finishes her figures.

Brannon, maybe.

Elysa, maybe.

April 21: Abstract Review


Elysa: It's better now, I wonder if I need to add more information for it to make sense to someone who hasn't read mypaper.

Habib:  I made two versions, one with numbers and one without.

Tony:  I'm not sure about my conclusions.  How to select keywords.

Brannon:  I don't have any specific questions.  No numbers.

Qingtao:  My abstract is 230 words and the limit is 150.  No numbers.

Haiyan:  I tried it two different ways because I am considering which data to include. I haven't decided yet.

Yang:  The limit is 200 words, and I didn't have enough room.  

Adam:  I think mine might be too short.

Monica:  Mine is at 250 words, maybe I could rephrase some things to include quantitative results.  I have 3 keywords, I could have up to 2 more.

April 23: Titles, Electronic Submission of Manuscripts

Status reports

Elysa:  aiming for mid-May (she's defending on May 1!)  May be interested in a swap.

Brannon:  aiming for late-May.  Reworking graphs, literature, a lot of work to be done.  Adding in more data.

Habib:  Monday, but he's still running with analyses.

Adidta:  Ready for Monday.  She still needs to review Haiyan's paper (by May 11).

Haiyan needs a couple of months to finish but will give Aditi a draft to read this afternoon.

Qingtao:  middle of May.

Monica is presenting at EcoLunch next week, which will help with feedback.  If she finishes by mid-May, her reviewer has time for it.

Tony has a defense on May 7, and will revise after that.  

Yang will aim for late May.  He is working on another paper with a co-author who is leaving town in may.

Adam:  Shooting for Monday.

Powerpoint slides are on my web site.

April 28:  Steps to Publication

Electronic submission of manuscripts