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FOR 694 Writing for Scientific Publication
Class Notes Fall 2015

Sept 4:  Why Publish?


Anayo, ERE, Vaccuum stripping ammonia recovery from wastewater.  Ammonium is an pollutant, very high in manure in dairy farming.  We want to develop a technology to help clean the environment and make some income (ammonium sulphate).  Vaccuum distillation, pH and T affect the solubility of NH4 (preventing NH3 volatilization).  TDS, total dissolved solids.

Tim:  Chestnut blight, genetic modification through tissue culture.  The growth form is important to their behavior in the field.  Tim will compare them to chestnuts of seed origin, hybrids crossed with Chinese, and Chinese chestnuts.  Study sites at Lafayette and Heiberg, shelterwoods or open fields.  14 different types.  Height, diameter, stem characteristcs.  Initial angle, present angle measured with an angle cube.  Stem straightness.  Canonical discriminant analysis, a multivariate technique.

Kristina:  Ratios of Cl-, Br-, and I- to identify sources to the T River.  East branch more agricultural, West more urbanized, effects of road salt.  Water isotopes for groundwater contribution.  Linear discriminant analysis.  End-member mixing.  Appalachian Basin brines describe natural sources

Kara:  Resorption is the process by which trees pull back nutrients from leaves before they fall.  Efficiency is the % pulled back from the green leaves.  Proficiency is the % left in the litter.  I have data from plots fertilized with N and P since 2011 in a 2x2 factorial.  Three stands for proficiency, one stand for efficiency (need green leaves as well as litter).  A previous study found that P resorption depended on soil N.  

Ehren: MS at Idaho, this is his second chapter.  Endophytes are symbionts that lives in plants, phyllosphere is the aboveground portion of the plant.  Fungi enter plants through the stoma.  Phyllosphere fungi are diverse.  Some are pathogens.  White bark pine is going extinct because of a fungal pathogen that causes white pine blister rust, which girdles the tree.  Four study sites across 30 miles in southern Oregon.  Analyze with molecular genetics, next generation sequencing, prevalence of taxa.  Elevation, height, aspect.  An operational taxonomic unit is like a species.

Eli:  Loss of indigenous wild edible plants, aim for an agricultural system based on native ecosystems.  Objectives: Study site purchased by his grandfather.  Split plot design, treatments  6 plots.  Plants Harvest.  ANOVA on site prep (burning), treatments, not significant.

Eugene:  Same location and experimental design.  My perspective is ecological restoration; his is ecosystem services.  At the point of agricultural abandonment

Why Publish?

Kristina:  If you have a new idea or a new technique, you get credit for it.

Kara:  To graduate.  To contribute to the wealth of knowledge.

Ehren:  Add building blocks to what other people can do going forward

Eli:  I just want to get out of here.  Contribute in the broader

Eugene:  I'm applying to PhD programs, publication is important to my CV.

Anayo:  To meet the requirements for graduation  If you don't publish it, it's like it never happened.

Tim:  To get the chestnut deregulated requires documentation, restore the chestnut.

Kristina:  Not all the salinity in rivers is from road salt, this provides a tool that other people could use.

Ehren: Applied aspect: Foresters want to create resistance to the white pine blister rusts.  My work could contribute to biocontrols.

Ruth:  Writing improves my understanding.  Peer review improves my papers.

Intro to Getting Started

Sept 8: Getting Started Exercise

What's hard about your paper?  How can we help you?

Kristina:  It's hard to know where to start; I've never written a paper before.  So far, I have a draft for settings and methods.

Ruth: See papers on my web site about writing a paper.  Share good ones that you find!

Eli:  Overcoming procrastination

Tim:  Getting started is harder than keeping going once you start.

Ehren:  That's a reason why outlining is helpful.

Eli:  Making conclusions was hard because my results are kind of bad.

Ehren:  My results were not as clear cut as I was hoping for.  It's difficult to interpret.  Hard to boil down to what's really important.

Tim:  Conclusions was the most difficult.  Everything I tried belonged in the results section.  How inclusive to be in the results.

Sept 10: Choosing your Journal

Factors to Consider

Reputation, Recognition: Impact factor (this uses a recent window and changes rapidly), name recognition.  What about a new journal started by an established journal.  Who the reviewers are.

Fit or Relevance to your field:  You want people to find your paper (maybe this is less important than it used to be).  Your paper will be rejected if it's not suitable to the journal you chose.

Read the scope.  You know what journals the papers you're reading are published in.  You know where your colleagues publish.

Special types of papers:  Notes, data, negative results, methods papers.  Reviews.

Acceptance rate:  Some journals put this on their web site.  Web of Science provides this.  Getting rejected delays publication.

Time to publication: Time from submission to acceptance.  Time from acceptance to publication (may not be an issue for electronic publication).  You can find these on papers if you don't find journal statistics.

Print or electronic: is anything print only?  Electronic access is important

Access:  Is it free for anyone to read it?  Subscribers only?  Some journals are entirely open access (PLOSOne, Ecosphere)  Citation rates are higher for papers published open access.

Color may cost extra

What are the submission rates?

Number of papers published.

Cost:  check, ask who's paying.  Which journals are free?

  1.  Commercial publishers don't charge authors.  They charge exorbitant fees to libraries.
  2.  Society journals are funded by membership.  Authors pay, subscriptions are cheap.
  3.  Open Access:  authors pay.  No fees to readers.

Coauthors may have an opinion.

Persistence:  Don't send your money to a predatory journal.

Journals you chose

Kristina:  Hydrological Processes.  It's free.  It publishes long papers.  My colleagues publish there.  Environmental Science and Technology has a higher impact factor.

Eli:  Agroecology and Sustainable Food Systems.  Scope is a good fit.  Check with co-authors.

Anayo:  Journal of Water Research.  Co-author input.  Strong impact factor.

Ehren:  Ecology (5.2).  Advisor preference, due to name recognition.  Forest Pathology or Phytopathology might be more realistic (2-3).

Kara:  Forest Ecology and Management has a wide audience, open to publishing negative results, results of local interest.  Rapid turnaround. Runner up:  Canadian Journal of Forest Research.

Tim:  Forest Ecology and Management, also considered Tree Physiology.  My paper has elements of ecology and management.  My advisor agrees.  I use papers from this journal a lot.

Read the instructions

Length:  JWR, Hydrological Processes <8000 words,

Abstract:  Ag and SFS 100, HP 300, JWR 250, Phytopath 300, FEM 400

Impact Factor: HP 2.8

Take a look for the statistics on time to publication.

Other:  FEM requires Highlights

Sept. 11: Figures and Tables

Print 4 copies at the size you expect the journal to reproduce them.

Please number your figures and tables so we can refer to them

Friday:  Ehren, Kristina, Tim, Bali

Color: Even if color is free in your journal, make sure your figures are legible in B&W (people print them and photocopy them, you hope)

Consistency in symbols is helpful

Close up space between panels if the axis labels are redundant and can be removed.

Two y-axis scales can be misleading (the comparison of scales is not meaningful)

Hollow symbols are better for seeing the density of observations if they overlap

Axis labels should be bigger than the numbers.  Bali says 18 pt Arial

Tables:  it's easier to compare numbers in columns than rows.  Think about transposing your tables.  Do response variables belong in columns?

Table vs. text?  When

P values to the 0.01 place or until the first digit.  When possible, report the P value, not just whether your result is significant relative to alpha.

Axes have to extend to cover your observations

Tuesday:  Anayo, Kara, Eugene, Eli

When to use bar graphs?  If stacking things that add!  And only for categorical x variables.

Box plots have more information.

When do you connect the dots?  Probably not for independent variables.

Labeling points in a figure!

Use the native units.

Use a log scale if it better displays your information.

When should your axes start at zero?  Is the magnitude of the effect relevant to zero?

Maps, could be inset.  Scale bar.  North arrow (if not up)


Sept 17: Outline, Objectives

Eli: it was hard to do the outline

Tim:  I struggled with how to start the discussion, but my advisor helped me.  What's the take-home from the results, anything unexpected, explaining, generalizing

Eugene: I tried one of the outlines on the web site.  Objectives, results to achieve objectives, discussion categories (interesting or anomalous, previous work, future work)

Ehren:  I need to condense my thesis into a paper, I found it helpful to put it in your template.  I have issues in the discussion, so that's where I can work on expanding it.  Abstract needs to be reduced by 50 words.  I changed journals.  I looked through Phytopathology and decided it would be better for a different chapter of my thesis.  The J of Fungal Ecology will be better.

Anayo: I looked at the journal requirements, and the template works.  The abstract requirements differ.

Kara:  I had already made an outline.  My proposal had an introduction that was too long; the outline helps me decide what needs to stay.  I think I disrupted the flow.

Please distinguish Results and Discussion.  Combining them is hard for beginning writers.

Bali:  My journal, Energy Policy, allows them to be combined, and this is conventional for my field.  I used the template with the document map. The journal requires a section on background information, economic context.

Kristy:  I used the template.  I don't usually use outlines, but this helped me take care of things I might have put off.  Abstract, Intro need work.  Discussion will be fleshed out later.

Eugene:  An annotated bibliography can help develop the intro and discussion.

Kristy makes her annotated bibliography in powerpoint, she can put images in there.

Citation management software:  Mendeley, Zotero.  Check them out.

Sept 22:  Results

Kristy:  Her advisor already saw it and identified that most of it was discussion!  So it went from 5 pages to 2 pages.

Kara:  I have a full factorial design except for an extra treatment in some of the blocks.  I don't know how to organize reporting the results.  I also have issues with how to order my results.

Suggestions:  Keep it in the same sequence as Methods and Discussion.  Start with the most important.  If it's boring, maybe you can put it in the Methods.

Anayo:  I'm still working on it.  Co-author wanted something else, which isn't done yet.

Eugene:  I have a problem with the statistics, beyond the problem with software on campus.

Ehren:  Could use tips on how to order things.  It seems long, could be condensed.

Bali:  I have a combined Results and Discussion section, which is how it will be submitted to the journal.  There are some concepts here that I need to review with an economist (David Newman, tomorrow).  Sentences could be improved.  I also still want review of my graphs and tables.

Eli:  My advisor suggested putting the figures in table format.  It makes my results section smaller, which is kind of sad.

Tim:  Mine is long because I have 10 variables and I address them individually.  They are similarly formatted, so you can focus on reviewing the first few.  The narrative seems choppy.  Is there a way to smooth it out?

Sept 24:  Methods

Tim:  I think it's decent.  I included the site characterization in the Methods even though my advisor thinks it belongs in the Results.  But then the methods for that follow the site description.

Eugene:  Methods is usually the easiest section for me to write.  It might be a little too brief, so I like to have other people look at it and see if they understand what we did.  I made a new table, because I thought the planting schemes were hard to explain.

He learned a new word "quincunxial". Should he use it?

Eli: It's a rough draft.

Ehren:  I have some results stuffed in here, which are diagnostic of the method.  I may have too much detail on the surface sterilization.

Kristy:  Mine was pretty straightforward, it's kind of boring.  I wasn't sure how much to include about how the multivariate linear discriminant model works.

Think about whether a reader needs this background to understand the results.

Bali:  I looked at other papers to see how they used the vector autoregressive model and how they described the modifications.  I'm concerned about how the subsections relate.  One test leads to another.

Kara:  I may have too much background in some places and not enough in others.  What to do about elements analyzed but not reported.  You can say not reported here. You could put them in an Appendix.  Or don't mention them.

Anayo:  It was not too difficult, I describe my setup and why I did what I did.  I reconfigured my setup at one point (the position of the vacuum pump and the height of the distilling column).  Do I need to explain this?

Ruth:  In the future, think about how you are going to write the methods before you do things that will be confusing to explain.  

Sept 29:  Writing

Kristy likes writing.  Writing this paper is hard compared to other things she has written in the past.  Why is it so slow?

Anayo:  I'm kind of lazy about writing.  It takes me a whole day to write half a page.  I think about what to write but what I write is not quite right.  Then I give up for the day.  It's challenging.

Bali:  Our first language is not English.  I think in Spanish and write in English.  When I went back to Puerto Rico I stopped talking English.  It was easier when I was here for three years.  The other problem is that I try to write the perfect sentence and spend 15 minutes on it.

Tim:  Writing is not my favorite thing to do.  I have productive days and not productive days.  The hardest thing is getting started.  So when I'm writing I try to get it all out and not be a perfectionist.  Then I feel good about being productive and afterwards I can try to edit it.

Eli:  I loathe writing.  It's my least favorite activity.  I hope this is the last thing I ever write in my life.  I'm going to be making a change after this.  

Ehren:  I've always liked writing.  Scientific writing is not like poetry, it's new and I'm rough at it.  The stuff I've brought in is too long; once I get started it flows fast and I say too much, like having discussion in my Results section.  Getting started is difficult, even with an outline.  I can't move on unless I'm happy with the first sentence.

Bali:  I like writing even though it's not that easy for me.  It's entertaining because it's challenging.  Other people need to understand it and want to read it.

Ruth:  What time of day is best for you to write?  What type of environment?

Smith and Brown

Why did you like Smith better?  Long sentences can lose the reader.  Paragraphs breaks are good.  Direct sentences.

We found the subject and verb of each sentence (easier for Smith than Brown) and then looked at some of our own sentences.


Anayo:  Practical English Handbook

Ehren:  Principles of Grantsmanship

Bali:  The Brief English Handbook, Day

Oct 1: Peer Review

Reviewer Assignments

Anayo reviews Kristy reviews Kara reviews Bali reviews Anayo.

Tim and Ehren review each other.

Eli and Eugene review each other.

Review Criteria

Criticize the science not the scientist.  You need the author's respect and appreciation.

Originality (we may not be the best reviewers to comment on this; think about who would be the best person to give you an expert friendly review)

Are the illustrations and tables necessary and acceptable?

Are the figures and tables properly related to the text?

Are the methods appropriate, current, and described clearly enough that the work could be repeated by another researcher?

Are the measurements in SI units?

Is the statistical analysis adequate?

Are the results presented in terms of science rather than statistics?

Are the conclusions supported by the data?

Does the paper tell a cohesive story? Is a tightly reasoned argument evident thoughout the paper?  Where does it wander from the story line?

Do the paragraphs flow smoothly

Is the writing concise, easy to follow, and interesting?

Is the English understandable to a multidisciplinary and multinational readership?  Be consistent in use of American or British English.

Eliminate jargon wherever possible.

Ratio of length to content.  Can you suggest any reductions in the paper or deletions of parts?  Is there unnecessary repetition?

Please make suggestions for deleting or adding references as appropriate.

Are the keywords and abstract informative?

Is the review of the literature limited to defining the problem.

Has the topic been put in context for readers who are not specialists in the field?

What makes a good review?

Start with your interpretation of the main points of the paper.  Establish credibility.  The authors can tell if they have not communicated effectively.

Give positive feedback as well as suggestions for improvement.

General comments are in narrative form, specific ones may not be complete sentences.

Try to be nice while getting your message across.  Avoid sarcasm.

Make suggestions for improvement to the message as well as to the presentation.

Detailed suggestions can be referenced by line number.

Make the comments as

The review process (for journals)

Author updates

Tim:  It's dramatically better than before.  I hate writing results, they never seem to flow.

Eli:  It's still a very rough draft.

Ehren:  It's looking better, shortened up in great ways, the reviews I've gotten have been super helpful.  The Discussion needs work because of material that used to be in the Results.

Ruth:  It's optional for reviewers to give comments on Intro and Discussion in this round.

Anayo:  I think I can improve it more.  I get confused about what to put in the Results, I think some of it might be Discussion.  It's better than before.

Kristy:  The abstract is too long.

Kara:  This is an improvement, I got a lot of comments on the Methods last week, they all improved my document except where I couldn't read handwriting.  I changed my Results a lot, I added September results and changed the order to start with the most important.  And I made new graphs in SAS that I'm really excited about, they look more professional than Excel graphs.

Bali:  I need my sentences to connect to the figures and tables.  Especially for the percentage change of some variables.

Oct 6: Statistical Considerations

Kristy:  linear discriminant analysis

Ehren: permutational multivariate analysis of variance

Eli:  ANOVAs with log transformation

Tim:  ANOVA and canonical discriminant analysis

Kara:  ANOVA and Pearson's correlations

Eugene:  ANOVA and t-test

Bali: vector auto-regressive model (multivariate time-series analysis), impulse response functions

Anayo: ANOVA

Oct 9: Introductions

What needs to be accomplished in an Introduction?

Problem statement

Background information

Justification for the approach

Objectives or hypotheses

Examples you brought


  1. Background, history of chestnut decline
  2. Background, site conditions for chestnut
  3. Background, comparison of seedling growth by species
  4. Background, field performance of seedlings
  5. Background, silviculture
  6. Problem statement and objectives

Good topic sentences.


  1. Background, fracking, takes half a paragraph to get to the reason we should care
  2. Background, flowback water
  3. Problem statement.  There are several challenges
  4. Previous approaches to the problem, why they are inadequate.  Justification of the study system.
  5. Objectives.  Methods to meet the objectives.  The paper focuses on developing the model, so methods are more important than in a conventional research paper.

Paragraph 4 could have been 2 paragraphs.


  1. Background on GHGs, EKC
  2. Justification for the study (one sentence reads like objectives).
  3. Challenges with causality testing, what is needed
  4. Objectives, includes a summary of key results, conclusions
  5. Table of Contents (not IMRD)


  1. Problem statement, invasive species
  2. Background, range expansion
  3. Background on Bromus tectorum (introduce the study species)
  4. Background on theory, relating back to paragraph 2
  5. Objectives, questions without answers, as is typical


  1. Background, N pollution,
  2. Background, resorption
  3. Problem statement, deficiencies in previous approach (soil nutrients)
  4. Alternatives to this approach (leaf nutrients)
  5. Justification for this approach
  6. Justification for this site
  7. Objectives, starts at the end of the previous paragraph


  1. Background on the species, lacking a problem statement
  2. Background on rhizomes and tubers, not clear what species
  3. Problem statement, no previous attempt (but why do we care?)
  4. Objectives


  1. Background on technologies, good problem statement
  2. Background on membrane distillation
  3. More on MD
  4. Types of MD
  5. Background on ammonia removal
  6. Background on a speciic membrane

7, 8, 9. Previous study on the topic

  1.  Sweep gas MD.  Justification for the approach
  2.  Problem statement, then Objectives.


Oct 15: Reviews, Responses to Reviews

Thoughts on the review process

Tim:  It was different, I'm not used to reviewing papers.  It was neat to see how much the paper had improved.

Eli:  It was really hard trying to be nice.

Kristy:  I went through and added please and if you prefer.  (Eli was joking.)

Kristy:  I wondered if I was being too nit-picky.  What if I would word something differently?

Eugene:  I mark up the hard copy, where I might suggest changing a word, but I wouldn't put it in the review document.

Ehren:  I did that, and the things that are hard to explain go into the written review.  In Word, you can track changes.

Ruth:  Reviewers for journals return marked-up Word documents.  If you want to be anonymous, you have to erase the properties for that document.  Instructions to reviewers mention this.

The journal will require you to respond to every point in the review.  So it's a pain if the reviewer is pointing out trivial corrections.

Some journals have copy editors (society journals).  Some journals do not.

Anayo:  This was not my area of specialization, so some of my comments might not be useful.

Kristy:  Some things I wrote as a question, some I googled.  I didn't know about diameter at breast height.

Bali: It's part of being an author and you have to do it.  Sometimes it's tedious and sometimes it's interesting.  You can learn new things and get ideas for new research.

Eugene:  You have to think about the paper more deeply than when you are skimming published papers.

Ehren:  The synopsis at the beginning of the review is a good exercise.  It's cool to get exposure to how other people design experiments and analyze them.  Expand your tool set.

Kara:  I wasn't familiar with the statistical tests and the acronyms; I asked questions.

Eugene:  This was different from my experience last year, because I'm involved with Eli's paper.

How long should we spend reviewing a paper?  Some reviewers spend more time than others.  Reading the paper once before beginning to make review comments is a common strategy. 

How are reviewers chosen?

For your final draft, you will include a one-page report on what will be needed to submit your paper.  Very likely, you will be asked to suggest reviewers (and reviewers not to assign).

Journals collect information on reviewers.

The Associate Editor selects the reviewers, possibly by looking at the papers you cite, papers you don't cite, people she knows, search terms for similar papers.  

How to write a response to reviews

  1.  It's important to include the review comments.  Some comments may require explanation.
  2.  It's important to document your changes.  Be specific.  Quote the changed material.

Some changes are so straightforward you can just say Done.

  1.  If you don't make a change, say so.
  2.  What if you disagree with a suggestion?  Explain why you are not taking the reviewer's advice.

How to show changes to the text?  Italics, indents, color...

Address your comments to the Editor.  It could go back to the reviewers; try not to insult them.

Advice to authors, using anonymous examples

Oct 16:  Discussions (examples)

What needs to be accomplished in the Discussion?

Interpretation of results

Justification for the approach (or does this belong in the Introduction?)

Background information (may belong in the Introduction)

Limitations of this approach

Comparison to other studies

Importance of the results

Applications beyond your study

Implications for future work

Wrap up the paper--Conclusion

Examples you brought


Note the use of subheadings

1-6 Interpretation of results, bringing in necessary background.

7,10 What's unique about this study

8,9 Interpretation, comparison to other studies

11-13  Limitations of this approach, advantages and disadvantages

14 future directions


  1. Results, comparison to other studies
  2. Results
  3. Results, comparison to other studies, interpretation
  4. Results, intepretation, comparison
  5. comparison, potential application
  6. explain unexpected result, compare to other studies
  7. background (could have gone in the Introduction?)
  8. future studies


  1. Background.  Intro to choosing end members.
  2. Background, why they chose the end members
  3. and 4.  Results and interpretation
  1.  New subsection, mini intro background, why we did this
  2.  Method
  3.  Results

8  More results and interpretation

New heading,

  1.  Interpretation
  2.  Background, site description
  3.  Interpretation
  4. Hypothesis!  methods, results, discussion

New heading,

13  Approach

14 Limitations

15 Limitations of inference, future work is needed.

16 Conclusions


  1. Results, As expected
  2. Background, should have been in the Introduction
  3. Background leading to the presentation of the result
  4. Results and interpretation
  5. Introduction to new topic
  6. Results and interpretation
  7. Results and interpretation, with comparison to other studies.
  8. Interpretation
  9. Results and interpretation, with comparison to other studies.
  10. New section, starting with results
  11. results, comparison, interpretation
  12. New section, Results, comparison, interpretation
  13. Conclusion, summary of results, ending w discussion.

Oct 20:  Discussions (yours)

How's the discussion

Eli wrote and outline but feels it's not ready for sharing.  Needs to regain momentum.

Motivational strategy:  Kristy uses as reward system, like a donut.  Or she can't watch a show or a movie until she finished.

Tim uses ice cream.  Finish a task by 10 p.m.

Kristy:  It's definitely different.  And she's trying a new model, on the advice of her advisor.

Anayo:  The Discussion was the most difficult for me.  The results differed a lot from our expectations, so I need to read a lot of papers to find an explanation.  What I did hasn't been done before.

Ehren:  It's more substantial now, now that I moved the comparison to other studies out of the Results and into the Discussion.  I find it helps to go work out, if I'm feeling stressed.

Eugene has been sick.  He has a paragraph..  He expects to have both parts done by Friday.

What he finds motivating:  Not to disappoint other people.

Tim brought the Introduction.  It might be too much information.

Kara: It's too long.  It's probably good for the thesis,

Oct 23: Introductions (yours)

Eli: It's not good and I hate writing.  

Anayo: It's not bad.  Writing the Discussion first helped.  I focused on what was relevant to my Discussion.

Kara:  My Introduction has been cut by half, compared to last week.  It's hard for me to read my own writing.  That's why I need a review.  Does it still flow, does it have anything to do with my topic?

Tim (discussion):  It's nice to finally have it on paper.  I got input from my advisor just this morning so it's still changing.  The last couple paragraphs are weak.

Kristy:  I don't particularly like it, but it does what it needs to do.  I had to introduce my approach, and it's boring.

Bali:  It's 4 pages long, it probably needs to be cut back.  It's a first draft.

Ehren:  Mine needs to be cut, if all that belongs in here is what it takes to lead to the Objectives.

Maybe some of it belongs in the Discussion.

Eugene:  This is one of the easiest papers I've ever written.  Maybe I've learning something.  It's concise.  Let me know if it's too concise and needs to be expanded.

Eli, too, may have areas that need to be expanded.

Oct 27:  Feedback for Improvement


Anayo:  I'm still working on it.  It's a busy week.  He might finish by Friday.

Kristy can finish by Friday.  Note that she is leaving Saturday at noon, returning Thursday.

Ehren:  It's taking way more time than I expected; I thought it was done, but no.  Taking things out or explaining why I added a study group. I redid my statistics.  Sunday or Monday would be better than Friday.

Eli would like to negotiate for a few extra days.  

Kara is having a hell of a time with the Discussion, it's not making sense.  I have 11 elements, I cut out 3.  

Kristy:  I cut out a lot of elements that aren't related to the story I'm trying to tell.  They were important for me to learn about the data set.

Tim:  I had productive day on Saturday.  I went to Panera and drank a lot of coffee.  I was going to leave after the easy edits on the Methods, but I stayed.

How to handle revisions

Kristy:  I've been doing the easy ones first.  The ones that take more time I need to set aside a day.

Anayo:  On weekends, get all the comments to look at at once.

Kara:  I keep multiple versions.

Ruth:  If you start at the end, you won't be changing line numbers for parts you haven't gotten to yet.

Ehren's ordination graph is a problem, has to be 3D.  PCA vs. NMDS, it's easier to explain.  

Mid-term assessment

  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.

For example:   3, 5, 2, 4, 1, 2, 4, 5,  (you each type one number)

and comments go after each heading

Sept 4:  Presentations.  Why Publish?

3,4,4, 4, 4,5,5, 5

Sept 8: Getting Started Exercise

5,5,5,5, 5,5,5, 5

Sept 10: Choosing your Journal

4,5,5, 5, 4,5, 4

Sept 11&15: Figures and Tables

4,3,4,5, 5,5, 4

Sept 17: Outline, Objectives

4,5,5,5, 4,5, 5

Sept 22:  Results

4,5,5,5, 5,5, 4

Sept 24:  Methods

4,5,4,5, 3,5, 4

Sept 29:  Writing

3,2,4,4, 2,4, NA

Oct 1: Peer Review

5,5,5,5, 4,5, 4

Oct 6: Statistical Considerations

4,1,5, NA, 2,2, NA

Oct 9: Introductions (examples)

4,5,1, NA, 4,5, 3

Oct 15: Reviews, Responses to Reviews

4,5,5, 5, 4,5, 4

Oct 16:  Discussions (examples)

4,5,3, 4, 3,4, NA

Oct 20:  Discussions (yours)

4,5,5, NA, 5,5, 4

Oct 23: Introductions (yours)

4,5,5, 5, 5,5, 4

Oct 27:  Feedback for Improvement

4,4, 4,5, 4

  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

Oct 30:  Peer Review (Readings)

4, 4, 4,3, 4

Nov 3: Ethics

5, 3, 4,4, 3

Nov 5:  Authorship

5, 3, 4,5, 3

Nov 10: Proposals

5, 5, 3,3, 5

Nov 12: Publication Productivity (readings)

5, 4, 4,4, 3

Nov 19:  Reviewer Help Session

5, 5, 5,5, 5

Nov 20: Abstracts (examples)

4, 5, 5,3, 4

Dec 1:  Help with Revisions

4, 5, 5,4, 4

Dec 4: Abstracts

5, 5, 5,5, 4

Dec 8:  Steps to Publication

5, 5, 5,5, 4

  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

I prefer working in pairs.

Working in pairs during class I think it most efficient.  Then when groups finish and there is time there can be additional feedback given.

This is one of the most useful aspects of this class. Triples can be more efficient if there are enough copies to go around.

Writing formal reviews out of class

no thank you. More time working on my own paper would be most helpful for me.

I don't think is necessary, just discussing improvements and things to change is most beneficial.

Peer review (one so far, one to go)

This is extremely helpful for me, both in learning how to read critically and review other's work as well as for the feedback that I receive from my reviewers.

Informal peer assistance outside of class

This can be done, but doesn't need to be mandatory.  Encouraging students to meet and talk about papers may be a good way to approach this.

Group discussion

seems to be working well - a great way to get the ideas flowing. What we do in class is sufficient for me.

Group discussion and going around the table definitely helps me participate and is helpful when we bounce ideas off of each other.  The couple of classes where there wasn't as much discussion (Examples of introduction and discussion) I found to be the least productive classes, personally.

Going around the table to equalize participation

It's good to hear everyone's perspective I think.

Class notes

I should probably make better use of the class notes. I can never seem to find the link when I think about it.


like the idea but too soon for another meal at 8 am. Rather not.

Perhaps for a Friday class, lunch potluck?

Electronic midterm evaluation   (last year was the first time)

This is an effective way to get feedback from the class and discuss how the class is going so far.

  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?

In some ways, I bet we are MORE effective reviewers because of our diversity and sometimes lack of knowledge about each other's fields. That way, we can gauge what audience our writing is appropriate for, and we can make sure that the points we are trying to make are getting through to a completely unbiased person. While we may not be able to make specific suggestions on content, we can still recognize good or bad writing, and give comments on whether something flows, is readable, etc.

I agree with the above statements. We will get reviews specific to our field of study from our co-authors, from the outside reviewers of our final drafts, and from the reviewers for the journal we send the paper to. 

for future classes with comparable diversity: spend time at the beginning of the semester teaching about different topics (e.g. key terms, share a paper or two from the field, typical figure from the field, etc. ).
Although there are many different topics within the class after the first couple of weeks you become familiar with the different papers.  I think it is helpful to have readers outside of the discipline to help determine if the paper can be read by a broader audience.

I think the presentation section should be more detailed including background information, methods, results and conclusion. 10min/ person. Emphasis on subject terminologies!

  1.  Other comments or suggestions

It seems that the way we already do things in class may be the most efficient. Some of the other ideas above are neat, but may be too time-consuming and/or not maximizing efficiency. I like that we start off as a group, going around the table, and then split off for one-on-one time with someone else in class. For me, personally, I am very busy this semester with other classes, so more work, like writing more formal reviews outside of class, I think would push me over the edge. I second that

Feedback with Anonymous Examples

Sentences about statistics can be rearranged to be about your study system.

"Time did not affect the change in mass loss with leaf litter type."

Statistics:  There was no interaction of time and litter type on mass loss.

Mass loss was consistent across litter types over time.

Don't say There was a significant effect of litter type.

Mass loss differed by litter type.Litter types differed  Elaborate

Direction is most important, magnitude is important, statistical significance is least important (as long as you don't describe insignificant effects.

Oak leaf litter decayed 23% slower than elm leaves (P = 0.03).

Reporting P values is more informative than using an alpha. 

There was a significant relationship between the observed and predicted percent lipid values via this method of estimation.

Describe the dependent variable as a function of the independent variable.

Predicted and observed percent lipid values were significantly related via this method of estimation.

Lipid values predicted by this method were significantly related to measured lipids.

Lipid concentrations were predictable from volumetric reactance in series (r2 = 0.88).

Oct 30:  Peer Review (Readings)

Peer review practices of psychological journals:  The fate of peer-reviewed articles submitted again.

12 already-published papers from 12 journals, changed the names and institutions (previously big names from famous places), journals have 80% rejection rates.  Only 3 were recognized by editors or reviewers as having already been published.  Of the 9, only 2 of 18 reviews were positive.  Statistics prove that this was not a random effect.  The review process is faulty, at best.  Then there is a whole packet of responses to this article.

Bali:  studs to duds 

The effects of blinding on the quality of peer review

The Journal of General Internal Medicine send 127 manuscripts to two reviewers, one blind and one not.  The reviewer does not know the identity of the author or the institution.  The quality of the review was scored by the editor and the authors agreed that the binded reviews were better.

Effect on the quality of peer review of blinding reviewers and asking them to sign their reports

The took a paper already accepted by BMJ, and introduced weaknesses.  They selected 420 reviewers, randomly assigning blinding and signing (full factorial).  The quality of the reviews was the same. Blinding reviewers to the authors identity were less likely to recommend rejection.  The rate of detection of errors was their measure of quality.

Comparison of self-citation by peer reviewers in a journal with single-blind peer review versus a journal with open peer review

Reviewers like to ask you to cite their papers.  If you argue against it, it reduces your chance of getting published. They analyzed all the reviews of papers in 2012 for two journals and compared them.  Of 155 papers accepted (334 reviews), 225 had reviewer citations in them.  94% of the recommendations were judged to be without merit.  And there was no difference between the two journals.

Trial set to focus on peer review

One biotech company's scientist reviewed a paper from a competing company, stole the information, and tried to patent it.  Is this legal?  In fact there is a law that protects the transfer of research to private law.  But we are supposed to decline to review if there is a conflict of interest.

Gender bias in the refereeing process

Editors of 24 primary research journals in ecology and evoluation requesting data on submissions and outcomes by gender.  7 editors from 5 journals complied. 2680 papers.  They didn't find an effect of gender of the first author.  Single-authored papers were rejected more often than multi-authored papers.  62 countries were represented, analyzed by income and English speaking (better acceptance rate even among wealthy countries).

How to write an influential review

There is a correlation between the detail and the negativity of reviews.

Advice:  Accentuate the positive.  Describe in detail what makes it good.

There is a bias against taking risks (proposals or papers), which inhibit innovation

The philosophical basis of peer review and the suppression of innovation

Quality control drives peer review rather than innovation.  Reviewers have lost touch with the goal of medicine.  Example from the discovery of Li for mental health.

People agree to do peer review for personal gain.

Eugene: how to better comunicate findings where they can be used.

Drawbacks of peer review

Letter to nature.  Three guys in Austria sent a published paper to 45 editors, and asked them to rate it in 8 categories, on a scale of 1-5.  14 declined, 31 editors ranged widely in their judgement, even in their evaluation of the linguistic merit for a paper written by English speakers.  The scientific merit was rated from poor to excellent.

Reviewer assignments

Anayo reviews Kara reviews Eli reviews Tim reviews Eugene reviews Ehren reviews Bali reviews Kristy reviews Anayo. 

Kristy's is done.  There is one analysis that she hasn't finished yet.

Eli has an additional analysis that will add a paragraph here and there.  In a week.  He's shooting for midweek.

Tim made it!  He stayed up late.  He completely redid his results. (It was a laundry list.)

I can't write results.  They don't make sense to me.  I don't know if it's good or not.

Ehren expects to have his done by Monday or Tuesday.  

Bali finished his, Ehren already has it.  

Kara is also shooting for the beginning of next week.  This class has been humbling, I was always confident of my writing but this is different from what I'm used to.  She shares Tim's confusion about writing the results.  What are they about, if not P values?  (see examples above from last year)

Anayo will try for Tuesday, and after that we'll tell him it's okay if we get it later.  He's meeting with his professor this afternoon.  Each time he sees him, there is always something new to do.

Eugene has a lot more lab work to do and he'll be doing analyses over Christmas break.  He needs to graduate in May.  He will give us a draft on Tuesday that describes what he has now.

Bali:  It's done, the parts are there, if it's makes sense, I don't know.  I need another set of eyes to look over it and tell me if it sucks or not.  Oversaturation (Ehren and Eugene agreed).  I'm spinning my wheels in the mud.

Ehren:  How do we get excited to keep working on a topic after we reach saturation?

Nov 3: Ethics

Retraction Watch Website

Outlier: 139

Kara: For root weights, it's easy to weigh them again.  Some were mistakes and easy to correct.

Ehren:  Depending on how to treat my results, I can get very different results.  For other people to be able to replicate the results, you want standard methods.  It was a crazy new method that led to the claim of cold fusion.  

If you do something different, try it the conventional way.

Kristy:  Usually, if it's an outlier, I can rerun it.  Watch the results so you can run it right away.  I still have one or two, and I leave them in my data set.  Iodine is high when it rains a lot; I think it's real.  I will discuss it in the Discussion.

Tony Federers  - Rule of Thumb--if covering a point with your thumb makes the pattern go away, don't put too much stock in the pattern.

Anayo has 5 replicates of his experiment.  One doesn't follow the trend.

Consider reporting medians instead of means.

If you exclude data from analysis, you need to describe this in your paper.  Use some easily described criteria.

Conflicts of interest: 142 industrial, 144  competition

Kristy sent links about Don Siegel being criticized for not disclosing his relationship to the gas industry in his hydrofracking work.  He does consulting and gets brought in as an expert witness.

GSA Annual Meeting 2015 (Baltimore, Maryland) opinion article

Syracuse.come news article

Waiting for patenting before publication is a bad deal for grad student.  In the case study, the student can't talk to the professor.

Who can you talk to if you have a problem with your major professor?  Other professors.  Department chair.  SU has an office with a third-party mediator.  

It would be best if you could tell the person you have a problem with.

Switching advisors could be a major setback.

At ESF, the Office of Instruction and Graduate Studies has responsibility for student-professor relationships.  There was an effort to create a policy about rights and responsibilities of grad students and professors, was it just signing it that made this fail last year?  Back in action now.

Allocation of credit: 145  

Authorship (credit): (146,) 147,

Jocelyn Bell and the discovery of pulsars.  Should she have shared the Nobel Prize with her advisor?

Grad students need lead authorship on papers, their advisors may have different interests.

Eugene did a project last year with minimal involvement from a second author, but two additional professors got added at the last minute.

The conflicts of interest are likely to be acute when the participants are institutionally (or psychologically) insecure.

More journals are requiring that the contributions of each author be described.

Misconduct:  148, 149, 150

A grad student exaggerated the status of a paper (listing it as submitted).  Plagiarism at ESF and failures to use the reporting system.  At ESF, we are going to have an investigation of the culture and reporting of cheating.

Nov 5:  Authorship

Author lists


  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

  1.  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.
  2.  Name your authors, in the order you propose to list them on your publication.
  3.  Does your list agree with any objective point system?  If not, what were the other factors that influenced your decision?
  4.  Who will you list in your Acknowledgements section?


Nov 10: Proposals

Eli will have a draft on Thursday for us to review.

Kara will have a draft today!  Two paragraphs still under revision in the Discussion.  It will be rough.

Anayo has one today!

What's in a proposal

Summary = Abstract

NSF requires separate sections for intellectual merit and broader impacts

Narrative = Project Description


Objectives, often with Hypotheses

Format them so they stand out

Number them and reference them often.

Hypotheses may be organized under Objectives

My rule is not to ask reviewers to remember more than 3 things.  Group them if you have to.

NOAA had  "Approach" with Hypotheses, Objectives before that.  

Rationale and Significance

Method, Experimental Plan

May be very detailed.  Justification for the approach.  Organize by objectives.  Future tense.  Don't forget to change to past tense when you publish.

Relate the measurements to the objectives (could be part of a data analysis section).

Project Management:  Who is doing what?

Timeline.  EPA, NYSERDA, contracts rather than grants.

Potential Pitfalls and Limitations

Alternative Approaches (appears to be required by NOAA)

Expected Products and Outcomes,   Project Deliverables

Results of Prior Support

Budget, Budget Justification

Detail in the budget justification can help establish your credibility and attention to detail and save you room elsewhere in the proposal.


Current and Pending Support   showing time commitments

Conflict of Interest: Coauthors, collaborators, advisees, advisors.  Same institution.  $ years for USDA, 5 years for NSF, keep a spreadsheet!  These people cannot review your proposal.

Biosketch, CV, Investigator Qualification

Yes, you can use this material again.  You own it, nobody published it.  If everything went according to plan (this never happens) you can use the introduction from your proposal as the introduction to your paper.

Deadlines:  Proposals have them.  Papers don't.

Length: 2 or 5 pages for a pre-proposal.  15

Line spacing: single

Font and margin requirements.  6 lines per inch.  

Reviewer Guidelines

importance, originality


Funding Opportunities:  

You can subscribe to an agency feed or a service, by categories or key words.  

Ask in Moon Library about opportunities specific to graduate students.

Nov 12: Publication Productivity (readings)

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

Productivity:  publications, grad students = f (academic rank (assist, assoc, full), gender, institutional affiliation, journals published in).

Full professors are the most productive.  

Among graduate students, women publish more than men.  Fewer women at higher ranks (in 2005).

Cumulative disadvantages in the careers of women ecologists (1993)

Productivity = papers, books, presentations, grants (these are all correlated), so they just used papers

Senior (average 44 years old) women 10.5, men 12.  Junior women (average 34 years old) 7.5, men 12.  

Motherhood and scientific productivity (1990)

Effect of having children, a previous study showed that faculty (social work field in the USA) with small children were most productive.  But in this study in Norway, women with small children were less productive, less so for men.  Better than women without children.  Having a partner is good.

Gender, household labor, and scholarly productivity among university professors (2000s)

Women spend more time on housework, and they spend more time on teaching.  No relationship between productivity and the amount of time spent on research!  

Time fragmentation hurts productivity.

Maybe women compensate by reducing their leisure time

Equity and equality in measuring productivity between men and women   (1998)

Women's productivity peaks later.  More co-authored papers.  More teaching and service.  They choose non-mainstream topics.  More likely to write books.  Women cite women, men cite men, and men get more citations.

They argue that productivity needs to be defined more broadly than publication impact.  Mentoring and teaching should be rewarded.

Changing patterns of publication productivity: accumulative advantage or institutional isomorphism?

Publication of papers and books: Faculty at doctoral universities, comprehensive, colleges, 2-year colleges.  Recognition accrues to those at the higher institutions.  Surveys in 1972, 1989, and 1992.  Publication rates were coming up at the lower institutions.  

Publish or perish?  Some reasons for perishing.

Publishing is important.  Advice: know the literature in your field, so you know what is novel.  Scientists are too critical of their own work.  If you wait for it to be perfect, you'll never publish it.  Some scientists are afraid of the criticism of the reviewers.  Other excuses.

Gender differences in India.  The cultural differences affecting women seem more severe than here (2002)  Women have a dual burden, work and family.

Nov 19:  Reviewer Help Session

Nov 20: Abstracts (examples)

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

Progress reports

Eli will hand off draft #2 before dinner on Thanksgiving Day or we will lash him with a wet noodle.

Tim is going through section by section, he got feedback on his capstone and from his advisor.  His thesis is due on Nov 30, two weeks before the defense.  After the defense and his revisions, he will submit the final draft to me and the expert reviewer.  Or we could review the same version as the committee.

Kristy already edited in response to review from us, then from her major professor (who wanted background related to geology) and now it's with the co-authors.

Ehren just got reviews from us yesterday, waiting on co-authors for feedback on the same version.

Kara is waiting for our reviews.

Analysis of Abstracts

What's in an abstract?

Problem statement (Background)


Methods if novel


Interpretation, Applications, Conclusions (Discussion)


ES&T has a graph in the abstract!  only 150-200 words.

  1. Background:  Problem not explicit
  2. Objectives (methods)
  3. Methods (study system)
  4. Methods (study system): ours is better.
  5. Results
  6. Interpretation.  Not written as a conclusion.


  1. Problem statement: why we care about chestnut
  2. Background
  3. Problem statement:  what's hard about fixing the problem
  4. Objective
  5. Methods

6-7 Results (soil)

8  Implications for management

9  Interpretion (light) or maybe a result

10 Implication for management


  1. Universal chestnut problem statement
  2. Background
  3. Problem with the solution
  4. Objectives or Methods
  5. Three sentences for results
  6. Interpretation, comparison to other studies
  7. Background relevant to implications
  8. Conclusion


  1. Objectives (long, run-on sentence)
  2. Results, 7 sentences, one includes methods, one includes some interpretation
  3. Implications (lots in one sentence)


  1. What they did
  2. Results (species)
  3. Results (deciduous vs evergreen).  Last sentence is interpretation
  4. Results
  5. Results
  6. Conclusion, Future research


  1. Problem statement
  2. Why it's important
  3. Objectives
  4. Interpretation and Implications

The ASA has a Publications Handbook and Style Manual on line with instructions about abstracts and a good example.

SUNY ESF College wid Metrics

Literature citation

Dec 1:  Help with Revisions

Status: How's it going?

Tim:  It's good.  I submitted my thesis to my committee on Sunday.  One suggestion was to include sketches of tree form, so choosing representative sketches of each type.

Eli is working on the discussion, which is meager.  He needs to just go work on it.

New York Times article:  Addicted to distraction, especially the internet.

Ehren:  Got revisions back from a co-author, too, who thinks it's ready to submit.  I could tighten up the Discussion a little more.  I have obscure species in the Appendix because I don't want to discuss them.

Kristy got edits back from Steve Shaw Sunday night.

She sent us material from a writing workshop, advice on writing each section of the paper.

Kara was waiting for comments from her reviewers, which she has now.

Eugene has been working on other things (applications).  

People who want another review:

Dec 4: Abstracts

Tim: Nothing in particular

Eli: It's the only thing I'm happy with

Anayo:  Nothing in particular

Ehren isn't sure whether to emphasize the relevance of his study to the forest disease.  I only used it because it was convenient.  But I think people will be interested in it.  
He can write more concisely than when he started this class.

Kristy: Mine has been revised a few times by my authors and my co-authors.

Kara:  Just read it.

Back to top

Dec 8:  Steps to Publication

Electronic submission of manuscripts

Make a one-page summary and upload it to our google folder:

Kristy: cover letter

This need not say more than "here is my paper."

Running head--the short title that runs at the head of a page.

Tim: -highlights- in addition to the abstract (Forest Ecology and Management)

Ehren also needs highlights (Fungal Ecology).  Nothing that wasn't in the guidelines to authors.

Dec 11: Final Drafts   Tim: after getting comments from the defense copy

Ehren: done

Kirsty:  done

Anayo is still doing an experiment

Kara's will be a Christmas present.

Eli's second draft will be distributed today, it won't have a Discussion.

Anayo:  Practical English Handbook