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FOR 694 Writing for Scientific Publication
Class Notes 2013

Class schedule                       



Assignments Due

Jan 15

Why Publish? 

Bring your questions

Jan 17

Discuss Getting Started

Getting Started Exercise

Jan 23

Choosing your Journal

Knowing your Journal Exercise

Jan 24

Figures and Tables

n copies of Tables and Figures

Jan 28

Figures and Tables

Jan 31

Outline and Objectives

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

Feb 4


Draft of Results (two copies)

Feb 6

Materials and Methods

Draft of Methods (two copies)

Feb 11

Writing exercise, in class

Bring a difficult section

Feb 14


Preparation for peer review

Editing and proofreading

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

Feb 18*

Statistical Considerations

Bring your questions

Feb 20


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

Feb 25

Advice, Responses to Reviews

First Peer Review Due

First Reviews.docx 

Feb 27


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

Mar 4

Progress on Introductions (shared in class)

2 copies double-spaced

Mar 6

Progress on Discussions

2 copies double-spaced


Mar 10-17 (spring break)


Mar 18

Mid-semester feedback

Anonymous feedback

Mar 20*

Readings on Peer Review

Submit  Rough Draft and Response to First Reviews

Mar 25



Mar 27


Authorship Exercise

Apr 1*


Bring examples of RFPs, proposals

Apr 3

Readings on Publication Productivity

Second Peer Review Due

Apr 8

Reviewer feedback and help session

Your review, your paper, or a section that needs help

Apr 10

Writing exercise, in class


Apr 15


Bring n copies of an example from your field

Apr 17

Work session

Sections for review

Apr 22

Abstract review

Title, by-line, key words

Abstracts due

Apr 24

Steps to Publication


Apr 29

Last Class (Final Steps)

Final Draft of Manuscript and Response to Second Reviews

Tues, January 15:  Why Publish?


Craig:  FNRM, foliar nutrient resorption in the context of nutrient limitation in New Hampshire.  Also working on a methods paper about filling gaps in hydrologic data sets.

Tingting: MS in GPES, Environmental Communication, role of social marketing promoting behavorial change.

Satish: PNW, Juneau, Alaska, MS, Environmental Science, Vidon MP.  Pre-commercial thinning in Tongass National Forest, effects on timber improvement and wildlife habitat.

Li: GPES, Stella MP, data set completed yesterday, need another week to finish the analysis.  Mechanical feedback between vegetation and fluvial processes.  Arizona.  Also a flume study in a man-made study in Minneapolis (10% to go).

Franklin: Yanai MP, 2nd year MS.  Distribution of two guilds of mycorrhizal fungal on roots in New Hampshire.

Nargis:  Russian from Tajikistan, MS, Environmental Science.  Sustainability of drinking water supply projects in rural areas.  

Sarah: first year, Vidon, stream channel geomorphology, riparian best management

Why Publish?

Li: My advisor says so

Craig: I spent a lot of time and effort (and money) so at least few people should be able to read about it.

Franklin: My first hit on google should be my work with fungi (not my work with fire).  To become a known entity in the field.  

Franklin:  To be more competitive on the job market, to demonstrate competence.

Nargis:  To expand my knowledge of the process of writing a journal article.

Tingting;  To advance knowledge in the field.

Satish:  Staying relevant, learning from the background literature review, context for your research problem.  

Satish:  Network of other researchers

Satish:  Personal goal, become a better writer.

Satish:  Qualification for career advancement.

Li:  I had a paper accepted yesterday, but it took two years to do it.  I want a faster way.

Craig: Smug self-satisfaction

Nargis:  Good for our CVs, and published papers count more than unpublished papers.

Tingting:  How the experience contributes to theory and how theory affects practice.

Nargis, Tingting, Craig, Li, Satish:  Improve the way people do things, researchers or resource managers.

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

Li:  Already on the third draft, with three co-authors.  The conclusions are hard--how to relate this to a bigger scale.  How to apply the theoretical research.  The other paper is in the stage of data analysis, with too many parameters in the model.

Craig:  How to frame the story, there are plenty of resorption papers out there already.  Writing it!  THis class will help.

Franklin:  I have non-significant results for the most interesting questions.  So it's hard to make an exciting story.

Nargis:  I had to change my research question at the very end.  Also learning to use the language of scientific reporting.

Tingting:  Just finished data analysis and results, which were not what I expected (not significant).  The discussion is going to be hard.

Satish:  I don't know the rules for publishing, style and politics.  Questions about authorship, guidelines for publishing.  Politically correct.

Li:  My supervisor changes what I write.  I want to write something that doesn't require so much revision.  

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

Li:  Already on the third draft, with three co-authors.  The conclusions are hard--how to relate this to a bigger scale.  How to apply the theoretical research.  The other paper is in the stage of data analysis, with too many parameters in the model.

Craig:  How to frame the story, there are plenty of resorption papers out there already.  Writing it!  THis class will help.

Franklin:  I have non-significant results for the most interesting questions.  So it's hard to make an exciting story.

Nargis:  I had to change my research question at the very end.  Also learning to use the language of scientific reporting.

Tingting:  Just finished data analysis and results, which were not what I expected (not significant).  The discussion is going to be hard.

Satish:  I don't know the rules for publishing, style and politics.  Questions about authorship, guidelines for publishing.  Politically correct.

Li:  My supervisor changes what I write.  I want to write something that doesn't require so much revision.  

Thursday, Jan 17: Getting Started Exercise

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

Satish:  Still waiting on data, and one of the treatments was a disaster (wind damage).  Hopefully this weekend

Tingting:  Just finished data analysis last week, and results were not what she expected.  Hard to match part 4 and part 1.

Nargis:  It was hard to remember what I was saying before, and now I can see that the conclusions weren't that strong.  I have a lot of methods and a lot of results.  The conclusions need to be stronger.

Franklin:  How to make my conclusions of broad interest.

Craig:  Which results to display, I have significant results by age class, or I could relate it to soils data, which was not as significant but more interesting.  Hard to decide what's most important to emphasize.

Li:  I'm still doing the data analysis.  In another week, she'll have them.  Temporal scale and spatial scale: which to emphasize.

Wednesday January 23: Choosing your Journal

Factors to Consider

Franklin:  Impact factor, given on the journal web site.  The factor describes how frequently articles are cited.  Some take self-citation into account.  Time is also a factor, for example for 2011, or a 5-year impact factor.

Nargis:  Prestige.  How do you know?  

Franklin:  Journals that are often cited in the papers you're reading.

Tingting:  Who is the audience for the journal?  In my case, social marketing, which journals do those people read?  If your keywords are in the title of a journal, that's a clue.  Franklin says the Canadian Journal of Botany is full of papers on fungi.

Craig:  Access!  If you can get Open Access for cheap, more people will read it.  $3000, $5000.

Craig:  Cost.  Some journals have page charges, even without Open Access.  

Subscription costs are something else, look for "page charges".  

Franklin:  You can make your thesis open access for $100.  

Franklin:  Why do we need the journals?  We could put our papers on the internet for less money.  Find your own peer reviewers.

There is a new model for Open Access that's all electronic with no subscription fees, but they might have a charge for the authors.  Isn't this better, if anyone who is interested can read it?

Nargis:  I looked at Sustainability Science Practice and Policy, they charge $1500 to the authors and the paper is available for free.

Ruth:  Some journals are restricting access only for a certain time period.  Maybe this is a good compromise.

Timing:  How long will it take your paper to be published?  You hear stories from other authors.

Journals care about this.  They want to report a short time to publication (and SSSAJ rejects and asks for resubmission, which restarts the clock and gives them a better statistic).

You can look at the date of first submission, sometimes revision and acceptance on the first page of the paper.  Craig has one that was accepted in 7 days!  It was a book chapter that was turned into a Mini-Review.  

Received Feb 8, accepted May 25, available on line June 6.

There is less problem now with a backlog at the journal, if they make the electronic version available immediately.  CJFR makes it available within 5 days of acceptance!

Craig:  New Phytologist will reject papers without review, this can be quicker than the review process.

Craig:  Probability of acceptance.  Journals may report this:

New Phytologist: 30%, World Development 40%, Ecology 15%.  Nature: 6.8%

You can send an email to ask for the acceptance rate, if you can find it, and we can make a graph.  Craig will send us a paper about this.

Nargis:  Some journals have word limits, consider the length of your article.  

Water Policy: 9000 words, abstract 200 words

CJFR:  20-page limit, 200 word abstract.  No precise limit for figures

Mycorrhiza publishes notes and editorials, with a max of 6 pages.  

Journal of Forestry limits the number of tables and figures.

Other requirements in the instruction: key words.

They may specify the organization of the paper.

They may tell you the format of the submission.



Journals you chose

Franklin:  Mycorrhiza, for the audience.  It's not as high impact as New Phytologist

Nargis:  Water Policy, for relevance, good impact factor compared to others.

TingTing: Social Marketing Quarterly, for the audience.

Craig:  Canadian Journal of Forest Research, right topic area, good reputation, previous work in my topic area was published there.  Might be easier than New Phytologist or Tree Physiology.  I'm also considering Ecosystems or Biogeochemistry.

Li:  Ecohydrology, because it's interdisciplinary, biology, ecology, and hydrology, so it fits the scope.  Impact factor is about right 2-3.  John Stella has published in it.

Figures and Tables

Jan 25:  Franklin, Nargis, Tingting

Table vs. Figure:  Can you find a way to

How to choose the order of non-numeric values?

-- Alphabetical adds no informatioin but is easy to look up.

-- In order of a numeric variable, in this case date of establishment or number of schemes.

No need to number entries unless you are referencing them somewhere else.

How to decide how many digits to report in numbers:  

-- you can use the variance to judge the precision of the mean

-- you should think about the accuracy and precision of the measurement

-- consistency across numbers (if units are the same)

Report 2 digits for P values unless they are both zero.

Graphing in Minitab, Excel, R, SPSS, SigmaPlot

We don't want to see evidence of defaults from your graphing software.

E.g. labels, shaded frames, outlines, where do tick marks go?

Group bars show that the observations you want to compare are close together

Graph theory packages, flow chart management

Box plots:  need to explain them in the caption

Show units in parentheses

Jan 29: Li, Tina, Craig

Color helps with legibility.  But color is expensive and you want people looking at a printout or a photocopy to be able to read your work.  Use color if it's free in the pdf version, but make sure it's legible in b&w.  Mycorrhiza requires a certain contrast ratio!  Use fill patterns and line types to distinguish legend entries.

Li:  Multiple variables on a panel, with different scales on right and left: readers see the two as related, so be cautious in doing this.

Use similar colors or symbol types to mean the same thing across your figures.

Symbols and fonts need to be big enough to be legible as reproduced.  Check your journal for size requirements.

Variable name (units):  Vegetation density (proportion of area with >50% cover)

The size of the symbol is rarely meaningful; use open symbols if they overlap; it's most important for them to be legible.


Mike Kelly: Avoid the unlabeled z axis (fake 3-D graphs)

Tufte: Don't use more dimensions in your graphs than in your data

When choosing how to group variables (e.g. pre and post contrasted, or youth and educator contrasted), it's easiest to compare observations in close proximity.  

Similarly, it's easier to compare numbers in columns than rows.  Think about what you want the reader to get out of it.  Commonly, comparisons are made between numbers in common units.

Franklin suggested "spark lines"

Jan 31: Outline, Objectives

Craig:  Organization comes after the writing process.  The paragraph-level outline will help.

Tina:  I start with a general outline, this was more detailed and might help.  I removed the objective that I couldn't meet.

Tingting:  In the past, I've used a traditional organization for an outline.  I tried one of the models on the web site, which is not in the same structure as the journal.  It's better to start with the results when you design your paper, though that's not the order we present it in.

Tingting:  There are elements in my study design that didn't turn out to be significant.

Li:  When I did my masters, I wrote all the Results first, and this was a barrier for my committee, who didn't want to read the whole thing.  So now I'm motivated to get in the habit of writing the outline first, for communicating with my co-authors.  They want to see the graphs first to understand the results.

Alex: The journal provided a template, with Methods at the end.  The reviewers complained about the order.  I needed to give more attention to the Discussion.

Alex: Writer's block: I'm intimidated by writing, so I read articles, take notes, edit, anything other than writing.

Craig: I aim for a first draft that's close to completion, and making every sentence sound perfect slows me down.  It would be more efficient to focus on the ideas first and not perfect the writing.

Tina:  My biggest problem is organization.  If I had the main ideas organized, I would know what direction to go.  

Tingting:  I have trouble with putting my thoughts in English.  I spent all day yesterday and got 300 words.  I can list out the main points, but I struggle to expand them.

Ruth:  There is no need to expand if you're not adding information.  Short is good!

What are the options for non-native speakers?  Google translate is not good, and it doesn't work to write in Chinese.

Alex didn't provide enough interpretation in his paper.

Tingting:  How to write a discussion that doesn't repeat the results?

Alex:  What belongs in the discussion section?  How not to repeat the introduction? Methods slip into the Results?

Craig:  It might even be relevant to address issues with the Methods in the Discussion.

Tingting:  Suggestions for improvements to the Methods will be in the Discussion.

Tina:  The Discussion is hard, I'm not finding comparable work to reference.

Tingting:  I found that attitudes are important, but other studies say they are not.

Kikang:  There is no treatment effect in my results.  Shall I describe differences that are not significant?

Ruth:  You need a different question!  You won't be reporting that result at all.

Tingting:  I have no significant effect of attitudes on fuelwood consumption; my advisor said I can describe the difference but say that it's not significant.  P = 0.08.

Tingting:  I did a path analysis, 10 times, removing insignificant variables.  How do I describe the process?

Feb 4:  Results

Tingting:  SigmaPlot is better than Minitab; Kikang helped me.  I checked the results.

Franklin:  My journal allows only three subsections: most authors use Introduction, Methods, then Results and Discussion.  I brought Results and Methods, but I'm not done redoing the Figures and Tables.  The results are very brief; should there be more?

Li:  The Results are mostly fine; I wonder if it could be shorter.

Alex:  I have time series, should I do statistics to see if they are statistically significant?  I have doubts about one of the approaches, using expenditures by the oil and gas industry and converting this to energy use.  

Tina:  I have both qualitative and quantitative data.  It's hard to present the qualitative data, there is so much information.

Tingting:  You could code them into themes.


Feb 6:  Methods

Tingting discovered Visio, which is free to ESF users, and will make her charts.

Tina:  Shall I cite what other people say about this method?

Do we need it to understand your paper?

Alex:  I think I'm missing data tables that would explain the sources of the numbers I'm using.

Tinting asked about moving descriptive information from Results to Methods.

Craig: Is there enough information to understand the stepwise regression in the Results?

Franklin: I used a logit transformation, which hasn't been popular for very long.  I explained this but I'm not sure it's important.

Kikang:  My methods overlap with my first paper.  Can I use the same methods section?  It's hard to make it different.

The journal of your first paper holds the copyright, so you can't reuse the text even though you wrote it.

Try writing a fresh section for your fresh purpose.  It will save you time and trouble.

Li:  I have trouble decided how much detail is necessary.  For example, how my material was packed and shipped.  Does the reader need to know in order to understand the results?

Feb 11:  Writing

What did you like better about Smith?  Active voice.  Paragraphs are good.  Maybe they shouldn't start with but or however.  Sentences are shorter.  Less use of technical language.

Exercise:  Identify the subject and verb of each sentence.  They should carry the meaning of your sentence.

Learning to be a better writer:  You can read books on writing.  You can read papers in your field.  You can read non-fiction and pay attention to the author's voice.  Alex likes Luminosity, but there's a risk of playing too much...  Other suggestions:  Coffee.  Take a break.  Give yourself an early deadline, so you have time to revise.  Get someone else to read your work (like someone from the Writing Center).  Know what time of day you work best.  Tracking your activities can help you learn how you're using your time.  

Feb 13: Peer Review

Reviewer Assignments

Franklin reviews Tingting reviews Tina reviews Alex reviews Franklin.

Kikang reviews Li reviews Craig reviews Kikang.

Review Criteria

  • Length relative to content?  
  • Is there unnecessary repetition in the text?  Is there duplication of tables and figures?
    Are the methods sufficient and adequately described?
  • Are terms well defined?  Is there unnecessary jargon?
  • Does the manuscript contain mathematics only necessary to make a point?
  • Are there any errors of fact, calculation, or interpretation?
  • Are all the figures and tables necessary?   Could they be better grouped?
  • Is the literary style clear?  
  • Would any of the text be clearer if condensed?
  • Is the manuscript logically organized?
  • Does the result answer the research question posed?  
  • Are the conclusions justified by the data?
  • Significance of the contribution, of broad interest, bridging a gap in knowledge.
  • Does the title reflect the contents?
  • Are the references adequate and up to date?  Can you suggest additional references?

What makes a good review?

The review is addressed to the Editor but will be shared with the authors.

Comments that are not important to the Editor don't need to be in your formal review.

The author will be asked to respond to your review.

Start with a summary of the paper you reviewed.  This demonstrates that you understood the paper.  

Major issues should be given top billing.

Give specific recommendations for improvement.  Line numbers help.

Comprensive and in the order of presentation.

Try to use positive constructions: The writing could be improved. not The writing is terrible.

You can comment on your qualifications as a reviewer.

Possible outcomes



accept pending revision

the paper could be sent out for a second review

Feb 18: Statistical Considerations

Alex: regression, time-series analysis, what about auto-correlation.  uncertainty and ratios.

Franklin: variable transformations and how to discuss them.  visual display of ANOVAs. repeated measures mixed models.

Kikang: ANOVA, repeated measures.

Craig: regression, time series.  ratios.

Li: non-parametric rank statistics.  Regression.

Tingting: path analysis, correlation, chi-squared, z tests.  Confirmatory factor analysis.

Tina: z tests, not sure for qualitative research.

Feb 20:  Introductions

What needs to be accomplished in an Introduction?

Problem statement

Why is this important?

Theoretical background

Other background, context

Explanation of terms

Reference to previous studies

Justification for this approach

Objectives, this should make clear what you are going to do


(opens with a quote from Yeats)

1.  The failings of predictive models for mutualism.  Problem statement.  

2.  Problem statement.  about theory.

3.  More background, coming up to date.  Narrowing in to the study system.

4.  Objectives.

1. Background, leading to problem, measuring nutrient limitation

2. Problem: need for a measure

3. Narrowing in to the study system: litter and nutrient resorption

4. Previous work, a controversy is introduced.

5. Importance of resorption

6. Minutia of resorption calculations: corrections for mass loss.  Is this important enough to be in the Introduction?  Could have gone in Methods.

7. Objectives.  Lists of what they did, last sentence states goals.


1.  Background, importance, and problem to be solved.

2.  Elaboration of the question (two components involved, root and microbial)

3.  About microbial response

4.  What they did, ending with specific objectives.

1. Problem statement:  How to make the learning of science more like the practice of science.

2.  Introduction to the Introduction (outline)

What is Authenticity?

3.  Definition of terms (authenticity)

4.  Importance, relevance

Maybe this section (3 and 4) was not necessary

Authenticity and Technology

5.  Introducing simulations

6.  Heavy or light reality

7.  Introducing handheld computers

8.  Justification for this approach

Participatory Simulations

9-12.  Previous work by this research team (Virus game)

13.  Problem statement: what the previous version lacked (authenticity)

Augmented Reality Simulations

14.  Next generation of game, Environmental Detectives (long paragraph)

15.  These games are more authentic

16.  Problem statement: missing feedback

Participatory Reality

17.  Goal statement

18.  What we did

19-20.  Research Questions

Feb 28: Reviews, Responses to Reviews

Thoughts on the review process

Craig: It took longer than I thought.

Alex: It took less time than I thought.

Franklin:  It was difficult to organize the response in a way that would help the author to see the overall structural issues first.  A list of details is easier.

Craig:  Next time, I would start with the details and tackle the big issues later.

Kikang:  It's hard to review a paper that's not in my field.  

Kikang:  When you criticise someone else, it helps you realize what you should have done.

Alex:  Even though it wasn't my field, I could reflect on whether the study design was adequate to test the hypotheses.

Tingting:  I lacked the background information to review the paper.  It will be easier next time when we have the rest of the paper.

Tingting:  When more information is needed, I can't tell what's missing.

Ruth:  Helping authors identify problems is helpful even if you don't know what the solution is.

Tina:  Because the paper is not in my field, I'm reluctant to give specific suggestions.  I said, I'm not sure, but...

Tingting:  It makes me a better author.  It's easier to see other people's mistakes.

Li:  It's hard to make constructive suggestions; it's easier to identify where I was confused.

Franklin:  Tone is difficult.  It's easy to be curt or overly terse, which could sound dismissive or derisive.  

Ruth:  Proofread, and look for opportunities to change negative constructions to positive ones.

TIngting: Start with positive.  

How to write a response to reviews

Your goal is to make a response document so complete that the AE doesn't have to go back to your manuscript.  

Start by providing the reviewers' comments.  Paste them into your response document.

You may need to provide the context for a review comment to be understandable.  It may be understandable in the context of the revised text.  If not, quote the original text.

You don't need to say much if you agree with the comment and can implement it. Done. Okay.

Make sure there's enough information for the AE to be confident of your change.

For substantial changes, you want to document your change.  It could be a description (label added to a graph).  You can quote the text, using quotes, and maybe color or a font change.

You might not take the advice of the reviewer, but then you need to explain why.  You may point to the answer elsewhere in the paper.  

Tone:  This document may well go back to the reviewers.  Be careful not to say that the reviewers are stupid.  Instead of "The reviewer can't spell, say, I can't find this in the dictionary. I'm not sure I understand the suggestion.

Fix something, if possible.  If you don't understand a comment, fix something related.

Thank you for pointing this out.

How formal do you need to be?  Informal could offend; err on the side of formality.

If whole sections have changed, you

The line numbers change as you edit your document.  Refer to the original.  Start at the bottom and the line numbers above don't change.  This can also help give you a more objective view of your paper.  You could start with the easy comments!

You don't have to document every change.

Major changes should be described.  Try not to make it sound like it's a different paper than the one that got reviewed.  

There is usually a deadline given for a response to reviews.  If you fail to meet the deadline, your paper could be treated as a new submission.  You should ask for more time if you're going to miss a deadline.

Advice to authors, using anonymous examples

Data is a plural noun.  Video-tape data was collected during the programs soils data was not replicated within a plot. This data was published in 2011 by Natural Resources Canada.

Adjectival phrases:

- and analyzed by using the student engaged learning in a technology rich interactive class protocol (Appendix 4). Analyzed by using the protocol for student-engaged learning in a technology-rich interactive class.

Stands are a middle-aged mixture of northern hardwoods.

Resorption efficiencies were calculated as the percent difference between fresh foliage and senesced litter nutrient concentrations. Percent difference between concentrations of nutrients in fresh foliage and senesced litter.

Significant digits:  post-survey mean is 10.95 out of 16 (68.43%).

Focus on results, not statistics: Path analysis identified a maximum likelihood solution for the study.  Significant covariance between education and age was identified.

Laundry list:  Help us see meaning in your results:

Nitrogen concentration in the Oa horizon had no effect on litter N, but showed a strong negative correlation with litter P (p=0.01).  In the B horizon, soil N was correlated with litter N at 0-10cm and 10-30cm (p=0.01).  B Horizon soil N was not a predictor of litter P at 0-10cm, but was at 10-30cm (p=0.05).  Litter P was positively correlated with P concentration in the Oe horizon (p=0.05), but showed no relationship with P concentration in the Oa and B horizons.

March 1:  Discussions

What belongs in these sections?

Interpretation of results.  Don't repeat your results.

Comparison to other studies.  Don't repeat your Introduction.


Implications for policy, management, researchers (methods)

Suggestions for future research, new questions.


When you reference your results in the Discussion, cite figures or tables.


  1.  Context of what has been done before
  2.  Overview of findings, description of the paper
  3.  Strength of this study
  4.  Summary of results
  5.  Explanation for a surprising result, suggestion for future work
  6.  Limitations
  7.  Implications for theory (behavior and values)
  8.  Implications for education


  1.  Explanation of the main result
  2.  Explanation or interpretation
  3.  Reference to other studies, contributing to the interpretation
  4.  Describe another result, compare to other studies, acknowledge limitation

5, 6, 7.  Explanation for a surprising result

  1.  More on vegetation and channel narrowing.

9, 10.  Limitations, ending with the assertion that the data are adequate.

  1.  Conclusions

Could have been more focused on the major points.  Some of this is not very relevant to the results.



  1.  Context, uniqueness of this contribution (mass loss correction)

subheading:  mass loss

  1.  Comparison to previous results
  2.  Justification for this approach: leaching
  3.  Another possible cause


5-8.  Relation to functional groups, KNP, growth, Ca


  1.  We found, in relation to others. Figure 5 for a new comparison!
  2.  Table 5 introduced, based on Figure 5.

subheading: climate

11-12.  Relation to other studies, interpretation


13-14.  implications for modeling

  1.  Conclusions (mostly summary)


Detailed interpretation and relation to other studies.

No limitations, implications, suggestions?

1-2  They had a problem with pre-treatment differences.

3  Importance of this approach.

Conclusions, including need for future research


  1.  Summary of a result, comparison to other studies
  2.  Another result, comparison to other studies.
  3.  Interpretation, comparison to other studies.
  4.  Introduces a figure reporting a result from a previous paper by the same author.  for interpretation.
  5. Interpretation (root turnover)
  6. Interpretation (specific resp)
  7.  Interpretation (TBCA)
  8.  Comparison to other studies (microbial respiration)
  9.  Interpretation.
  10.  Conclusion (mostly a summary of results), end with implications.


March 4:  Introductions

Li:  I lost track of what I actually want to say in the Introduction.

Make an outline of what you have, see if this helps you reorganize.

Tina:  I have multiple ideas to introduce (education, technology)

Craig:  How should I sequence these topics?  If I start big and narrow in, it takes a long time to get to my topic.

Franklin:  My introduction to my specific study is good, but linking it to the big picture is not a straight path.

Alex:  I have the context but not the statement for what I did.  Need to add objectives.

Kikang:  How much detail to provide?  I'm also having trouble deciding how much to specify in the hypotheses.  

Li:  List only the ones that are justified by your introduction

Craig:  If there are too many details, try to generalize about them.

Tingting:  How much should I emphasize the location of my study?

Tingting:  Some of my citations of the literature weren't under

Li:  Where should I introduce the novelty of my study?  Now it's in the last sentence of each paragraph.

Tina:  I put it at the end of my introduction. This new approach can solve these problems.

Franklin:  Here's the problem, here's the gap, here's the solution.

March 4: Discussions

Li: It only takes half a page to make my main points.  How much detail do I need in my explanations.

Tingting:  I have one paragraph on my main results, then I have a paragraph on each of the factors.  It comes to 12 pages; is this too much detail?

Tina:  I have recommendations based on the different sections of the results.  The order is not exactly the same as the results.  Each paragraph has results, relation to other work, and recommendations for the future.  Is this too many recommendations?

Kikang:  There are too many possible explanations for my results, I can't decide which are relevant.

Li:  Sometimes the results are not so strongly linked to the conclusion or recommendation.

Alex:  I don't discuss explanations for the trends.  There are confounding factors, such as the price of oil, that might contribute to our observations.  

Franklin:  How should I end my paper?

Conclusions should link back out to the big picture.

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?  1,4, 3, 1, , 1,

Good for starting, not useful for writing, fun conversation, but we already knew we wanted to publish

Getting Started  5, 5, 4, 5, 4.5, 4, .

Extremely useful.  Gives an outline for the abstract.  Communicate the overarching idea.  Very useful to organize my paper at the beginning.  Clarify the objectives, good idea to focus on results first.  Could be ordered 3, 2, 1, 4 (starting with results)

Choosing your Journal  2, 4, 3, 3, 4, 1.5

Valuable information I did not know about.  Suggestion:  Provide a table with the criteria to use to compare their journal choices, include links to citation index information.  Classmates are unlikely to be familiar with the journals being discussed.  The process is common.

Figures and Tables  3, 5, 4, 4.5, 3, 4, 5

Useful to compare figures and tables.  Feedback helpful.  Hard if you're not ready for it.  Difficult, feedback important.  There should be a list of do's and don'ts, like for the writing.  How about a graph that has all the possible mistakes.

Outline and Objectives  5,4, 4, 5, 3, 4, 3

This is like getting started, useful for organizing thoughts on the paper.  Getting comments is good.  Redundant with getting started exercise?  Is there a way to develop this from the GSE?

What about Figures&Tables, then GSE and Outline?  You need the focus of the paper before you can do the Figures&Tables.

Results (yours) 4, 4, 4, 4.5, 5, 5, 4

Having a due date is good.  Short is good.  Having many reviewers is helpful.  Starting with the Results was a good strategy.

Materials and Methods (yours)  4, 4, 3, 5, 3, 5, 4.5

Reviewers can identify omissions, which the author knows too well.  The class doesn't approximate the journal audience.

Writing exercise, in class  1, 4, 3, 5, 5, 3, 4

Fun, helpful, well structured.  Length vs. content issues.  Provide links to resources about writing on the web site.

Preparation for peer review  3, 4, 3, 5, 5, 4, 4.5

Examples are useful.  Q&A about the publication process.

Introductions (examples)  2, 4, 3, 5, 2, 5, 3

Better to pick a good and bad example?  We didn't have enough time to spend on each one.  It's helpful to have identified an exemplary introduction.

Discussions (examples)  2, 4, 3, 5, 2, 5, 1.5

This is a little harder than the Introductions, because the Discussions refer to other parts of the paper.   The person presenting could show how the Discussion relates to the rest of the paper.

Examples should be selected based on criteria for what belongs in the Discussion.

Would it help to read the Discussion from the same papers as the Introductions?

Statistical Considerations  3, 4, 4, 4, 4, 3, 5

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.

Responses to Reviews  3, 4, 4, 5, 3, 3, 4

Good for learning about the peer-review process.  Important skills.

Progress on Introductions (yours)  4, 4, 3, 5, 4, 3, 3

Due date!  An early draft helps identify what needs to be done.

Progress on Discussions (yours)  4, 4, 4, 5, 4, 3, 2

  1.  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                  1, 4, 3, 5, 3, 4, 3

3/25:  Ethics  2, 3, 4, 5, 5, 3, 2

3/27:  Authorship  2, 4, 4, 5, 4, 3, 2,

very important, but might not require an entire class period.

4/1:  Proposals  3, 4, 3, 4, 2, 4, 4

4/3:  Readings on Publication Productivity 2, 3, 3, 5, 3, 5, 2

4/8:  Reviewer feedback and help session  3, 4, 4, 5, 3, 4, 5,

4/10:  Proposals  3, 4, 3, 4, 3, ?, 4

4/15:  Abstracts (examples) 3, 4, 3, 5, 5, 5, 2

4/17:  Work session  5, 4, 3, ?, 5, 3, 5

4/22:  Abstracts (yours)  5, 4, 4, 5, 5, 4, 4

4/24:  Steps to Publication  4, 4, 4, 5, 5, 3, 4.5

4/29:  Last Class (Final Steps)  4, 4, 4, 5, ?, 3, ,

  1.  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  4

Useful.  Hard when we don't understand the papers.

Writing formal reviews out of class

Useful, including ability to write reviews.  Limited by expertise, outside our field.

Informal peer assistance outside of class

Good, approachability.

Group discussion  4

Helps me feel like I'm part of the process.

Going around the table to equalize participation

Can feel forced.  Depends on how many we are.  Hard to be last.  Get all the perspectives.

Class notes



Great, 4, maybe,

  1.  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?

Less would be better.  No, diversity is good.  Outsiders can ask us, Why is this important? Divide into Social sci vs. natural sci.?

Presentations?  4, 1, 2, 2, (4)

  1.  Other comments or suggestions.

Some people have more experience with writing papers, make use of that.

Sessions on conference, posters, and presentations.

Session on tools:  Software for referencing, organizing references, tracking journals and articles in my field.  Research Gate.

Other software:  graphics, statistics.  This should be early in the semester.

March 22:  Second Draft

Craig: New data, statistical input, now everything is changed.

Franklin: My reviewers suggested statistical tests that I have not completed.  The results could change!  Another suggestion was to use the basal area by species.

Alex:  Reviewers are asking for more detail on the data and the calculation.  Some of the data are iffy.  I haven't see the raw data, in some cases.  Someone does have the data but isn't allowed to share it.  The owner of the data is asking for payment ($17-27 per table).  (Li: collaborate with people who have the data.)  The data are shown in a report.  Yes, read the values from the graph in the report!  This doesn't answer the question of how the values were processed.

Kikang:  I have new results and my paper has changed a lot.  The reviews were helpful.  How could I have missed that part?  Half of the reviews are no longer relevant.

Li:  I have the same problem.  What should I say?  This result was removed from the paper because

Tingting:  I revised a lot, it's 30 pages now instead of 75.  Reviewers asked for definitions, so I added to the literature review.  I cut a lot from other sections.  The comments were very helpful.  My reviewers didn't like the lengthy section on objectives and hypotheses.

Tina: My committee is flexible about the format of the thesis.

The changes were extensive, so I wrote an overview of my changes, which precedes the detailed responses.  What should I do if the reviewer is not correct?

If you can, change something to prevent a future reviewer from making the same mistake.

Li: I spent most of my effort on the Methods and Results, and I have more detail now (the main story didn't change).  I want to work on the Conclusion and send the paper tomorrow morning.

Reviewer assignments

Alex reviews Li reviews Tina reviews Tingting reviews Kikang reviews Franklin reviews Craig reviews Alex.

Potluck Planning

Friday March 29 7p.m.

Franklin:  Mushroom hors d'oeuvres

Tingting:  beer

Kikang:  something Korean

Craig:  dessert

Tina: something Chinese (edible and good)

Alex: Soup (Canadian)

Ruth: Bread, cheese, wine

At Alex's 521 Clarendon

March 29: Ethics

Outlier: 139

Normally you would go back to investigate an outlier like this.  Two outliers, of 8 observations!  

Some reports include statistics run on both the full and the selected data sets.

If you exclude observations, you must report your rejection criteria.

Conflicts of interest: 142, 144

For proposal review: same institution, coauthors (e.g. last 4 years), major professor, advisees

Problems with commercial interest: competing firms.  Intellectual property rights.

Allocation of credit: 145

Ben describes his new method to another scientist who implements the method and publishes it without acknowledging Ben.  

Errata are published to correct errors in journal articles.  Omitting someone from the acknowledgements probably wouldn't warrant publication of an erratum.

Alex reports a similar experience with a non-sponsor who reported the results of the report that they withdrew from sponsoring.

Is there a safe way to share results before publication?  Ben didn't need to give all the details.

Authorship (credit): 146,147,

Misconduct:  148, 149, 150

Fabrication: A student creates a citation for a grant, the paper has not been submitted.  The student is dismissed, the story appears to be about institutional policies regarding academic integrity.  

Falsification: Don't do it.  But what if someone else does?

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.  


April 1:  Authorship

Tina:  There will be 2 authors, me and my MP.  The other two committee members earned 10-20 points.  Game design was a big part of the study, is this another category?  Or you need to give extra credit points to acknowledge more major contributions.

With two authors, your paper would appear in text as Hua and Folta 2013.  If you add any more authors, it will be Hua et al. 2013.  How might Folta feel about that?

 Tingting:  Me, MP, two additional committee members.  These authors will be included even though they haven't contributed much yet.  They might contribute more.  My MP told me to include them.  She thought that even the statistical advisor should be an author; this seems too low a bar.  Acknowledgement should be enough.

 Franklin:  Diggs, Yanai, Horton.  Horton needed 5 bonus points to make the threshold.  
The point system allows each person to contribute up to 100%.  We can make judgments about relative contributions at a finer scale.  Also, the categories are equally weighted, while they contribute differently to different projects.

Do co-authors get more credit for being higher on the list?  Sometimes the last author gets more credit than the other junior authors.  

What about effort that didn't pay off, does that still warrant authorship?

Some journals have a section on Author contributions where you can explain who did what.

Craig:  It depends on whether we use Melany's data.  See, Yanai, Quintero.  If Fisk, ask her whether she prefers to be first or last.   


Tina: Tom Hughes was my boss last summer, he will review, he was involved in planning and execution.  Maybe he'll be an author.  There was a graduate student who provided the content for the game.  He also helped develop the questionnaire.  Don Leopold reviewed the survey, too.  I also got help with English language editing in the game.  The IRB person.  Classmates who gave feedback.  Statistician.

Tingting:  This work would not have been possible without... 

Don't include co-authors in your Acknowledgments.

 Don't forget funding sources.
 Craig:  Bill O'Neill for digestions, Matt V. for soils data.  Corrie Blodgett, was she involved?  Field crews that dug soil pits.  

April 1: Proposals

What's in a proposal

Intro and Methods are similar to a journal article.  Heavier on the justification.

In the case of a renewal proposal, there will be results.  

Expected results.

Are Methods last?  

Usually there is an abstract, unless the proposal is very short.

Length is prescribed: use all the space you've been given; you'll be criticized for not providing enough information.

Sections may also be prescribed.

Conflict of interest: list of people who won't be asked to review your proposal.

Budget and Budget Justification.

Table of Contents

CV (Biographical Sketch for NSF)



 RFPs (Requests for Proposals)

Confidentiality:  Reviewers are required to destroy proposals after reviewing.

Selection criteria, description of the application process.

April 7:  Peer Review (Readings)

Craig read two studies about blinding in peer review (JAMA, medical).  

Mcnutt et al (1990): each paper was reviewed by two reviewers, one knew who the author was and one didn't, both could choose whether to sign their reviews.  127 consecutive manuscripts submitted to JAMA.  Editors rated the quality of the review (scale of 1-5), as did the authors.  

The Editors said the blinded reviewers were better at reviewing methods, importance, key issues.  The quality of the presentation was not different.  The authors didn't rate blinded and unblinded reviewers differently.  Blind is better.

Godlee et al (1996): They took published papers and introduced 8 weaknesses, then got 420 reviews (blind to author, signed, full factorial).  Blinding and signing didn't affect the success of the reviewers at finding the errors.  The mean number of errors found was about 2!  


The peer-review process is weighted towards quality control, which suppresses innovation because innovators aren't good at quality control.  There should be more risk-taking in the review process.  Then there are many examples of important papers that were rejected because of quality control issues.  Historical perspective, suppression by QC is getting worse.

Both male and female reviewers are review papers by men more favorably than papers by women (so blind review is better).

Non-native speakers are less likely to get papers published.  How much of this is fluency and how much is bias?

Reviewers are biased favorably if their work is cited in the paper.

Tina: A Troubled Tradition

Trust in the review process, ethical issues.  A reviewer could steal the ideas in a paper, delay reviewing it, and publish the ideas.  Suggestions for alternative forms of peer review:  double-blind, open review.  Researchers are not trained to be good reviewers.

Franklin: Court case, a reviewer stole a DNA sequence and patented it.  Is there a legal basis for the confidentiality of peer review?  We don't know because the case was settled out of court (for $21 million).

Who are the peer reviewers and how much do they review?

A study compared reviews by authors and non-authors (why?)

Negative reviews are longer than positive reviews.  Maybe we should try to describe in detail what makes it good.

April 8: Help with Revisions

Status: How's it going?

Craig:  Second draft will be done this week.  Franklin could review the Methods today.

Franklin:  Would love to have another review.  A committee member suggested another approach.  Continuing battles with R.  A week or two from now would be good.

Alex:  Probably next week.  Has something to work on.

Tingting:  Focusing on the Discussion section, adding material suggested by her advisor.  Could use help deciding what's relevant to a journal article as opposed to the thesis.

Li:  I thought I would be the last!  I need to review the paper and make the conclusions more persuasive

People who want another review:

April 15: Abstracts (examples)

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

Progress reports

Franklin is motivated by guilt.  He needs to do a Friedman test, but he's encountering errors in R.  He needs to schedule time with the person who offered to help him.

Alex is redoing all his calculations from scratch, so he can better describe where the data came from and what he did.

Tina needs to recode her qualitative analysis and have someone review it.  Her co-author agreed to review the coding, she needs to meet with her.

Li, spatial autocorrelation seems like an issue, but other studies do a sensitivity analysis.

Franklin: those corrections and transformations never seem to matter.

Li needs help with grammar.  Tina makes appointments with the writing center at SU (you're allowed up to 2 hours per week).  The SU center uses writing professors.  The ESF one uses students; some are better than others.  Tina has three favorites at SU.  Tingting has a favorite at ESF, who now knows her work.

Franklin suggests Lang-8, an online service for language learners.  You can short post clips and you'll get three people responding within the afternoon.

Analysis of Abstracts

Alex:  EROI of Norwegian Oil and Gas.

Introduction could be more compelling.  No statement of objectives.  Results are clear.  Is the conclusion justified by the results?

Franklin:  New Phytologist requires bullet points in a summary instead of an abstract

Rationale gives background but doesn't say why it's important.

Objectives, hypotheses.

Methods are missing!


Conclusions, addresses the hypotheses.


Background, definition

Problem statement: surprising dearth in the literature


This is a review paper, so it doesn't have Methods or Results.

Maybe knowing something about the scope (methods) of the review would have been helpful.


Problem statement, need for environmental education in Madagascar (too grand?)


Product, extracurricular programs (could have a better match with the problem statement about new locations)




Conclusions, implications, it does go to new locations


Background without telling us what the problem is.  What's unknown?



Results (lots)

No conclusions or implications or importance.




Problem (Unfortunately)

Fortunately (methods)




Last sentence--?




Red flag










Last sentence - a model is proposed could be more informative.

April 17:  Publication Productivity (readings)

Franklin:  Publication Productivity among Scientists, Mary Frank Fox (awesome)

Inverse square law:  half of the work is done by the square root of the population of publishing scientists.  (differs by discipline)

Psychological variables: dominant persons not overly concerned with other people's lives or approval.  Strong egos, more attached to their work than to people.  Eminent scientists do their best writing in the morning.  

Age: Productivity peaks in the late 30s or early 40s and a second peak in the early 50s.  (based on a study in the 1950s, may not be a lot of women in that pool)

Environment: More important where you do your graduate work than where you're hired thereafter.  If you move to a major institution from a minor one, you are likely to be productive.

For people who remain in academia, productivity is motivated by peers, for those who leave, they are motivated by citations, over the long term.

Productivity is correlated with communication with colleagues, e.g. attendance at conferences.
 Craig:  Changing Patterns of Publication Productivity: Accumulative Advantage or Institutional Isomorphism? Dey, Milem, and Berger

Accumulative advantage:  People from prestigious places get more resources which gets them further ahead.

Institutional isomorphism:  Institutions are structurally similar and converge in productivity.

Publication rates over time, in Carnegie categories of schools, reflect cumulative advantage.  

Li: Equity and Equality in Measuring Faculty Productivity, Creamer

Universities should have a better reward structure; current structures favor men.

Female faculty teach more classes, they write more books rather than papers, they do more mentoring, and peak later in productivity.  But faculty productivity is based on publication.

Other papers about gender differences:

 Women who have children have lower productivity, when the children are less than 10.  After that, they are as productive as men.

Interviews of 673 faculty members: women do more household labor than men.

There are plenty of women now in ecology in graduate school but not in the faculty ranks.

Studies of cohorts of scientists and where the women fall out of the pipeline.

Language in reference letters differs for men and women, which biases the hiring process against women.

Publish or Perish: Some Reasons for Perishing

The work is no good, the scientists are lazy, too self-critical, fear criticism, or make excuses.
Bias against people who aren't married with kids.

This is a big problem in Asia.

April 22: Abstracts

Status reports

Franklin:  DSE, dark septate endophytes, have been added to the paper.  Friedman was also suggested.  Other VA structures.

Tingting: Someone at her presentation on Friday asked a tough question about the path analysis, she hadn't interpreted the results correctly.  She checked her analysis and it's true.  So she has to change her interpretation.  Whom to ask for help?  Co-authors.

Li:  If I have trouble understanding my results, I go back to the data.  Sometimes I find mistakes.

Franklin:  Check for a correlation with income.

Tina:  She had 13 high school students at Clark Reservation last week, two more coming up in the next two weeks.  She could add more data, and she has advice on a better analysis.

Franklin:  Include it in this publication if it will make it better.  

Li is working on grammar corrections.  She is focused on her candidacy exam.  


Li: Already has co-author input

Tina did hers based on our last session.

Tingting:  How much detail to include?  Steering committee preferred the version with more detail.  250 word limit.

Franklin: 150-250 word limit.  Trends but not numerical results.

Craig:  150-250.  Writing a poster helped my abstract.

April 24: Titles, Electronic Submission of Manuscripts

Google Doc

April 29:  Steps to Publication

Status reports

Franklin is going to add a figure, having difficulty Friedman in R (could abandon R?)  Li has done the Wilcoxon ranked test in R.  Cleaning up the text.  Finish by the end of May.

Alex:  Draft number two will be delivered to Craig and Ruth by May 3.  Discussion was weak.

Craig did another analysis this weekend, which changed some of the results, strengthening some points but not others.  Rewriting.  Aiming for May 7 (when he leaves for NH) for the second draft to go to Franklin and Ruth.

Tina has one more group tomorrow, so she will have more data in her final draft.  She will have the final draft by June 10, for Eric Klopfer.

Li will take an incomplete because she is preparing for her candidacy exam, and she will have feedback from her advisor.  Aiming for July.

Tingting is giving her capstone this week and her defense next week.  So the end of the third week in May would be after she gets feedback from the committee.

Electronic submission of manuscripts

Suggestions for next year

Food in class!

Organize a potluck early on.  Otherwise we get to know one another only through criticism.

Team-building exercises?  Ropes course!

Books:  Craig, Alex: Strunk and White,