Skip to main contentSkip to footer content

FOR 694 Writing for Scientific Publication
Class Notes Spring 2015

Class schedule                  



Assignments Due

Jan 13

Why Publish?

Background presentation (5 minutes)

Jan 15

Discuss   Getting Started

Getting Started Exercise

Jan 20

Choosing your Journal

Knowing your Journal Exercise

Jan 22

Figures and Tables

n copies of Tables and Figures

Jan 27

Figures and Tables

Jan 29

Outline and Objectives

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

Feb 3


Draft of Results (two copies)

Feb 5

Materials and Methods

Draft of Methods (two copies)

Feb 10

Writing exercise, in class

Bring a difficult section

Feb 12


Preparation for peer review

Editing and proofreading

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

Feb 17


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

Feb 24

Statistical Considerations

Bring your questions


Feb 26

Advice, Responses to Reviews

First Peer Review Due

Feb 27


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

Mar 3

Progress on Introductions (shared in class)

2 copies double-spaced

Mar 5

Progress on Discussions

2 copies double-spaced


Mar 10-14 (spring break)


Mar 17

Mid-semester feedback

Anonymous feedback

Mar 19

Sections in need of feedback

2 copies double-spaced

Mar 24


Submit  Rough Draft and Response to First Reviews

Mar 26


Authorship Exercise

Mar 31


Bring examples of RFPs, proposals

Apr 2

Readings on Peer Review

Second Peer Review Due

Apr 6

Readings on Publication Productivity

Reviewer feedback and help session

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

Apr 9


Writing exercise, in class

Bring n copies of an example from your field

Apr 14

Abstract review

Title, by-line, key words

Abstracts due

Apr 16

Work session

Sections for review

Apr 21

Zotero by Allison (Ruth in DC)

Bring your computer

Apr 23

Steps to Publication


Apr 28

Last Class (Final Steps)

Final Draft of Manuscript and Response to Second Reviews


Tue, January 13:  Why Publish?



How to know the age of eels without killing them.  Life cycle of the American eel.  In November they were listed as endangered by the IUCN.

Silver eels (mature) are not well understood.

Methods:  electrofishing, Fyke netting.

Take measurements that might indicate maturity.  Eyes and fins get bigger before they go to sea.

Biochemical impedence as a non-destructive method of measuring fat content.

Compare these to destructive internal measurements.


American chestnut blight, development of transgenic resistance (as opposed to backcrossing with Chinese chestnut), using an enzyme from wheat that breaks down oxalic acid.

Goal: get determination of non-regulated status by USDA APHIS.

Two projects:  Compare leaf litter decomposition rates, what fungi are involved in decomposition.


Also American chestnut.  Allison grows the chestnuts in tissue culture.  How to get them to root better.


Sustainability of green infrastructure projects in Syracuse, stormwater management.  Porous pavements, green roofs, rain gardens.  Save the Rain, $80M project, saving combined sewer overflow into Onondaga Creek and Onondaga Lake, better than building more sewage treatment and storage capacity (gray infrastructure) in poor neighborhoods (social justice).

Emergy:  (H.T. Odum) embodied energy, all sources converted to solar emjoules.

Transformity: ratio of energy in to energy contained?

Sustainability depending on source of the energy?

Examples of various green infrastructure projects, documentation involved.


Polycyclic aromatic hydrocarbons (PAHs).  Combustion.  Incomplete combustion PAHs.  They absorb on particulate matter:  PM 2.5 (smaller than 2.5 um, ends up in your lungs)

Collect them in an impactor, separates fine from heavy particles, Teflon filter.  Extract the PAHs in DCM, analyze with gas chromatography and mass spectrometry.  Compare composition to cancer risk assessment.  Sampling sites on Jahn laboratory, elementary school across I81, and Heiberg Forest (less PAH, same PM).


Phosphorus limitation in Adirondack Lakes.  N limiting in terrestrial ecosystems, P in aquatic ecosystems.  N deposition from air pollution decreasing since the Clean Air Act.  Will N become more limiting with less N deposition?  Using lake chemistry data from ALTM (Adirondack Long-Term Monitoring), distinguishing seepage lakes (with no outlet) and drainage lakes, including chain draining lakes and differences in till depth in the watershed.

Gram:  Why the Adirondacks?  Granitic bedrock.


White pine regeneration from direct seeding.  White pine is slow growing and hardwood seedlings overtop it if the site is good for hardwoods.  Test rates of overstory removal, site preparation (scarification) at two sites differing in site index (Pack and Huntington).  Huntington's site index is 82, Pack 52, and 55 is the point above which it's hard to grow white pine.  Put out seed, monitor for 2 growing seasons.

Cutting at Pack was bad for seedlings, it's too dry if they aren't shaded.

Statistics are tough because the df are so low.


Field testing chestnuts: seed origin, tissue-cultured transgenics, and tissue-culture controls.  The transgenic trees don't grow normally.  Bifurcation ratio (branchiness), other metrics.

Allison: There is a plot with transgenic plants with seed origin.

Why Publish?

Amanda:  I want to combat the public perception of GMOs.

Sarah:  I want managers to use my research results.

Eugene:  Promote green infrastructure to decision-makers.

Jackie:  Promote the value of long-term data (decision-makers)

Quincey:  I owe it to my advisor; the project funded my education.

Tim:  Help the production of chestnut, move towards seed origin.

Gram:  Add Syracuse to the nexus of data that currently exist.  We see LA and NYC, and Syracuse is a more interesting case study.

Allison:  Fame and fortune.

Allison:  If my results have been through peer review and been accepted by a journal, my committee will accept them.

Amanda:  I can contribute to an argument in the scientific community (about the role of fungi)

Sarah:  The experience of peer review will improve my work.

Eugene:  I put all this work into it, why not get more credit.

Jackie:  Bring new ideas to the scientific community

Quincey:  Make my parents proud of me.

Gram:  Future funding

Allison:  Improve procedures for the research community.

Thu, Jan 15: Getting Started Exercise

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

Amanda:  Most difficulty with the conclusion (sounds like results).  Unexpected results.

Sarah wasn't sure which thesis chapter to work on with this class.  She will start with the methods paper on bioelectrical impedance analysis.

Quincey:  I'm an awkward writer and I know it.  It will help me to have someone else look at my writing.

Gram:  Bridging the gap between the results into the discussion to make a cohesive statement.

Ying:  Long-range transport of ozone.  Issues with writing and with distinguishing results from conclusions.  How to make the introduction interesting to a broad audience.

Jackie:  I have too many results and I need to decide which ones are most important to include.

Eugene:  It will be hard to get my paper down to a reasonable size, because I did 16 separate emergy analyses and I want to compare them.  I need to restructure my data, which will be a pain.

Tue January 20: Choosing your Journal

Factors to Consider

Amanda:  Journals that I cite most frequently

Jackie:  Impact factor.  Citations per paper.  

Gram:  The citations of a paper are not always indicative of the quality

If the status of the journal affects your citation rate, that would be a good reason to choose it.

Quincey:  The acceptance rate may be low for the most prestigious journals.

How could you find the acceptance rate?  If it's not on their web site, write to the editor.

Ying:  Choose a journal suitable for my results (novelty).

Gram:  Subject matter, appropriate audience.  Some of the atmospheric chemistry journals are about the physics, which my paper is not.

Eugene:  I looked at whether journals had published on emergy before.  I want to reach urban planners, and the journals they read are not typically publishing on emergy.

Ruth:  The editor who handles your paper may not know this, so put it in your cover letter.

Amanda:  The cost of publication.

Ying:  International journal, published in English.  More people can read it.

Quincey:  Access to the journal.  Open Access articles are available to anyone.  What about the other journals?  

Gram:  ESF has fewer subscriptions than Rutgers did.  If we get it, it's pretty accessible.

Qunicey:  USFS authors can post their publications.  

Ruth:  Think about your author list.  USFS authors, UC author gets Open Access with Elsevier.

Open papers get more citations.

Ask your co-authors for their opinions.

Time to publication:  This may be on the web site.  

Reputation, Authenticy (there is a lot of marketing of electonic journals that may exist or persist).  If it's indexed, it's been through some kind of approval process.

Eugene:  I need a journal that supports electronic appendices.

What about building your CV?  

Journals you chose

Eugene:  Landscape and Urban Planning: fits the scope, published a couple of emergy articles, medium in reputation and I didn't want to aim too high.

Sarah:  Fishery Bulletin, published by the National Marine Fisheries Service, NOAA.  On line since 1881.  It doesn't have the greatest impact but it's respected with the audience I want to reach.

Quincy:  New Forests.  Since 1980s.  Specific to afforestation and reforestation.

Gram:  High ball would be Atmospheric Environment.  I can afford to get rejected (2nd PhD student).  If not, Aerosol and Air Quality Research.  

Ying:  Atmospheric Environment.  

Jackie:  Ecological Applications, depending on the direction of my discussion.  If not, Biogeochemistry.  

Amanda:  Soil Biology and Biochemistry had 4.41 IF, aim and scope: they say that they are interested in the introduction of GMO in the soil environment.  My paper on fungi could go to New Phytologist, but they don't want leaf litter (good thing she read the instructions).

Read the instructions

Ecological Applications:  IF 4.13, 30% acceptance, $75/page.  4 months.  350 word abstract.  Prefers Discussion to be combined with Results.

Biogeochemistry:  IF , 23% acceptance

Landscape and Urban Planning:  IF 3.07, 21% acceptance.  13 weeks for review, 4.5 to publication after acceptance.  4000-8000 words.  250 abstract.  Figures and tables should be used with economy.

Atmospheric Chemistry and Physics:  25 euros/page if in LaTeX, 30 if in Word.  30 MB.  Figures not to exceed half a page, minimum of tables.

Atmospheric Environment:  $1000 per paper (Open Access). 6500 words.

Fishery Bulletin:  10-15 ms pages, full papers are 20-30 pp.  150 or 250 words, short or long papers. Number of figures not more than 1 per 4 pages of text.

Springer link:  no cost unless for Open Access $1-3K.  90 days for New Forests.  150-250 word abstract

Soil Biology and Biochemistry:  short communications are <1200 words, 3 printed pages. Abstract not to exceed 10% of the length.  No length specified for full articles.  Conclusions can have a subheading, not a heading.

Elsevier: no cost, $2500 for Open Access

Atmosphere:  32 days for a decision

Archiving: SB&B, lots do it.

Other requirements:  Keywords, Research highlights.

What about a graphical abstract?  Video abstract?  Thumbnail?  What??

It's good to be prepared for all you will be asked for when you are finally ready to submit.

Figures and Tables

Thursday:  Allison, Gram, Amanda, Ying.  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

Find out whether you can have color in your figures.  If you do, test them by printing in black and white.  Red and blue might look exactly the same after someone prints it or photocopies it.

Consider stacked panels if you have common axes.  If so, you save on legends.

Defaults from Excel: remove the box around the figure.  Do you really want gridlines?  Force trailing zeros if you want them.  Decide if you want the top and right of your plot area boxed.

How many digits?  The precision of the measurement.  There may be other uncertainties; what is your confidence in the estimate?  Look at the variability across the measurements.  Follow conventions: With a P value give one digit but at least to the hundredths place.

Gram has composite samples, it looks strange to show a time series with steps, but do what your readers are accustomed to.

When using names that are meaningful only to a small audience, think about whether you can use names that will be meaningful to your readers.  Wild type rather than Boar.

Think about the order of class variables and names.  

Align numbers on the decimal point.

Be careful about curve fitting.  If you can, show your data.  If you fit a curve, say how.

Tuesday:  Jackie, Quincy, Sarah, Eugene

Maps:  be selective about what you include.  You need a scale bar.  You need a north arrow, especially if north is not up.  Beware of the aspect ratio.  Do you care about political boundaries?  (Do they help readers know where you are?)  Think about the base map.  

Your journal may support appendices: think about putting detailed background information into a an appendix.

Most journals don't allow vertical lines in tables.

If you start tables in Excel, then copy to Word or Powerpoint, you have more control over formatting.

Should lat and long be in degrees and minutes or UTM?  See if your journal specifies.  We think lat and long is still more conventional

Be careful about interpreting differences between statistical significance and non-significance.  Test whether the two relationships are signficantly different from one another (they may not be).

R2 and P values in the caption or in the figure?  People look at the figures and don't always read the caption.

We saw examples of informative captions.  A affects B instead of  A as a function of B.

It's easier to compare numbers in columns than rows.  

Jan 29: Outline, Objectives 

Sarah:  I'm currently focused on the results, so my Intro and Discussion don't have the broad perspective that that they will later.

Jackie:  My Discussion has very broad ideas, I need it to relate to my results.

Amanda:  I have trouble deciding what to include, I have eight nutrients and three years of data.

Quincey:  My ideas in the Discussion are not as well developed.  This exercise made me go back to my lit review.  I need review of my objectives to see if they make sense to other people they make sense to me.

Gram:  My results are interesting but I'm looking for something emergent of interest beyond the case study.

Ying:  My draft has the results and discussion together.  The discussion compares my results to those of other studies.

Eugene:  Discussion is the weakest section now.  It's different reporting to the sponsor than to the scientific community.

What does a Discussion need to do?

Relate results to a bigger picture

Compare results to previous studies

Limitations of the research

Explain anomalies

Interpret the results

Implications for management

Suggestions for future research


Amanda doesn't usually use outlines, but it was helpful for thinking through the Intro and Discussion.

Jackie uses outlines, but not at this level of detail for all the parts at once.

Quincey:  There is a helpful link on the web site, asking questions like the Getting Started Exercise.

Feb 3:  Results

Jackie:  The results are just a list without the discussion.

We discussed the separate vs. combined Results and Discussion.

Sarah:  This was a productive exercise.  I'm still tweaking the results.  Is it understandable?

Ying:  I have a lot of information, I keep writing more and more and more.  I have too many details.

Gram:  I pulled the results from a combined results and discussion section.

Allison:  I'm not sure all the figures are necessary, if they could be said in one sentence of the text.  I cut my experiments down from 7 to 4.

Figures attract more notice.  Decide based on how important the point is.

Good experience with stacking graphs.

Amanda:  Also deciding whether to include a figure.

Should I change the form of the sentences that are presenting results of similar structure?

See Fowler elegant variation (actually, this is about vocabulary, does the same apply to sentence structure?)

Feb 5:  Methods

Enough for another scientist to replicate your study.

Enough for the reader to understand what you're doing.

Gram: I used a lot of EPA methods, try to keep out the minutia but still describe the method.

Amanda:  How much to describe equations?  How much is common knowlege?

Previous example:  The volume of a cylinder is not interesting to

Alison:  If someone in my lab has published this before, how much do I need to describe?  Generating shoots from embryo lines is not easy to explain but it's not very relevant to my study.

Jackie:  My methods were statistical, but I have to describe how the data were collected.  It's more important to describe the lakes than the analytical methods.

Sarah:  How much detail?  We're so close to the methods it's hard to take a step back and judge.

Ying:  My study is data analysis, I cite the sources of the data.  There are many choices of satellite observations for CO; I use MOPITT.   

Eugene:  My analysis is based on information that other people collected and it's not all from one place.   

Feb 10: Writing

Eugene:  Technical writing is challenging; I want it to be more concise.

Amanda:  Being specific about what you're saying and cutting out what's unnecessary.

Jackie likes writing and editing and she likes honest critique.  Organization: what is the best order?  Are my ideas communicated well.

Gram:  I could make my sentences more accessible to the reader.

Ying: I make grammatical errors without knowing it.  I have a hard time describing the figures; sometimes I say too much and sometimes I don't point out the most important point.

Sarah likes writing. Sometimes she doesn't explain enough and sometimes it's too wordy.

Alison likes writing (she even writes fiction).  Methods and results are straightforward.  Introductions are the hardest.  Looking up references is distracting.

Eugene has tried annotating a bibliography first.  

Jackie cuts hers up and arranges it into the narrative flow.

Smith and Brown

Active voice:  The subject is doing the action.  Some professors want the passive voice.

Use short sentences.  Paragraph breaks are good.

Feb 12: Peer Review

Reviewer Assignments

Eugene reviews Gram reviews Ying reviews Jackie reviews Sarah reviews Amanda reviews Allison reviews Eugene. 

Review Criteria

(Is the subject within the scope of the journal?)

Does the paper tell a cohesive story?  Is a tightly reasoned argument carried throughout the paper, or does it wander from the argument?

Is the arrangement logical?  Could specific sections be added, deleted, or moved?

Can the manuscript be shortened without losing its impact?

Is the description of the methods sufficiently informative to allow another researcher to replicate the results?

Are all measurements reported in SI units?  (depends on the journal)

Are the illustrations and tables necessary and acceptable?

When results are started in the text, can you easily verify them by examining tables and figures?

Relevance and understandability to a broad audience?

Clarity of writing?

These questions will be more relevant to your next draft

Does the title clearly and sufficiently reflect its content?

Does the abstract tell in brief the reasons for the study, the methods, the results, and the conclusions?


Does the author distinguish between conjecture and fact?  Is the amount of conjecture excessive?

Are the conclusions supported by the data?  Are they consistent with the objectives?

Is the number of citations appropriate to the subject and length of the text?

Are all and only pertinent references cited?

Is it new and original? (not for a review article)

More advice to authors

Comply with the instructions to authors for your journal.  

Use past tense for results, present tense sounds like a generalization.

What makes a good review?

Start with a description of the paper.  Show that you read and understand the paper.  This establishes credibility?

Put general comments first.  

Detailed comments should be referenced by line number.

You can give positive comments and not just criticisms.

You will likely give feedback to the author that's not important enough for the editor to see (e.g. spelling errors).  Advice not worthy of a response to the editor.

Point out where a reader not familiar with the study could be confused.

Try to suggest solutions when pointing out problems.

Use - I statements: I found this to be confusing rather than your presentation is confusing.

Ask questions.  Maybe better than -I found this confusing - you can ask - What were you trying to achieve?

If you know enough, you can make very specific suggestions on relevant literature.  

Third person is easier to take if the comments are negative.

Both the editor and the authors are important audiences for your review.

The review process (for journals)

Author updates

Sarah:  Still working on it

Ying:  Will retrieve and improve hers.

Eugene:  I'm reworking my methods section, the version reported to the agency wasn't in the right format for the journal audience.

Allison:  I thought I had it, but I'm going to add line numbers and resubmit.

Gram:  My graphs didn't print out the way I expected.  

Amanda will add line numbers.  I'm still doing lab work for another paper.

Jackie:  I thought it was good, and last night I got another data set.  

Feb 19: Introductions

What needs to be accomplished in an Introduction?

Problem statement.  Why is this important?  Not too technical at the start.

What has been done before?  What is new in your study?

Background necessary to understand the study

Introduction to the sampling site--when does this belong in the Methods?  You all need to introduce your subject of study.  If you can justify why this site is the best place to conduct this study, include it.  

Objectives.  There should be no surprises by this time. 

Check also that concepts you want to bring up in Discussion are introduced at this time.

Let's look at the logical connections.

Examples you brought


  1. Importance, problem
  2. Problems with previous approaches
  3. Introduction to the proposed new approach
  4. Objectives, in the form of a summary of the approach and analysis 


  1. Background on the problem.  History.  Nitrogen
  2. Previous studies, specific to the region studied.
  3. Introduce nutrient limitation, phosphorus.
  4. Lake studies and P limitation in lakes
  5. Approaches to assessing N vs P limitation
  6. Objectives, with 4 numbered hypotheses

Maybe they could have warned us earlier that they are studying both foliage and lakes.


  1. Introduce transgenic trees, fate of organisms, interactions with others including soil organisms.
  2. Background on soil food web
  3. Previous work in this topic area (but we don't yet know what their study system is), chitinase.
  4. Pleiotropic effects (other properties may be affected)
  5. Introduce the species of study and the gene (chitinase) that was introduced.  It was hypothesized previously?
  6. Objectives, except that it starts with Besides and has a background sentence in the middle.


  1. Introduction to PAHs and why they are important.
  2. Introduction to Hong Kong as a case study.  They didn't tell us why we should be interested in Hong Kong.
  3. Previous work in Hong Kong, limitations of previous work, objectives in the last sentence.

They could have put more of a health emphasis.  Atmospheric Environment has short introductions.


  1. Problem statement, food production and sustainable agriculture.
  2. Indigenous agroforestry for sustainable agriculture, ends by introducing emergy work.

3-8.  Introduction to the group studied and their agroecosystem, one paragraph for each stage.

Where are the objectives?

  1. Last paragraph defines emergy, says it can be applied (not phrased as an objective).


  1. Introduction to ozone and previous studies on Asian sources and impact on North America.  Last two sentences sound like objectives.
  2. Background on ozone photochemistry.
  3. Objectives, with an index to the sections that follow
  4.  Limitations of this approach (should be discussion?) and some elements of selection of the methods.

Feb 24: Statistical Considerations

Gram:  SE, uses duplicates

Sarah:  linear regression, cluster analysis and PCA

Jackie:  Kendall's tau, linear regression

Amanda:  ANOVA, Tukey tests

Eugene:  ANOVA, Tukey, pairwise comparison

Allison:  ANOVA, Wallace-Duncan K ratio

Ying: cluster analysis, linear regression, Kendall test

Feb 26: Reviews, Responses to Reviews

Thoughts on the review process

Sarah:  I hope that it was helpful.  If it's not in my field, I might not know if a method was done correctly.  I could comment on clarity.

Eugene:  I could help with formatting and consistency.  Asking questions about things that weren't clear.

Gram had knowledge in some areas, which helped him give advice.  

Jackie:  I found I didn't have many general comments, most were copy editing.

Ying:  I couldn't give good suggestions, but I could ask questions about the logic of the paper.

Allison:  I went for the big questions.  It was fun to learn about something totally different.

Amanda:  I don't know if my suggestions are relevant, so I qualify them.  We don't know what's been done already.

Amanda:  This helps me look at my own work critically.

Eugene:  It gives me ideas for structuring.

Gram:  I had a complete paper to review.  I will have to think about the overall structure as I write.

How much to recommend style or provide editing?

Reviewers vary a lot in how much detailed copy editing they provide.

How to write a response to reviews

Start with a copy of the reviews, and add your reponses.

Don't wait until you have made all the changes.  If you start at the bottom, the line numbers will remain relevant.  Keep a copy of the version you submitted for reference.  You can compare documents in Word to see your changes.

How to open your review?  Address your comments to the editor.  

Thank the editor and the reviewers.  You can ask for the identity of a reviewer to add them to the Acknowledgments.

Distinguish your comments from the reviewers comments.  Italics, color, bold, or Comment and Response.  Consider spacing.

What if you get a stupid suggestion?  Be polite.

What if the change is trivial?  You can just say, Corrected. Fixed. Done.

Often, the reviewer has misunderstood the paper.  Don't say, "They were wrong, we were right."  Try to make a change that will prevent a future reader from having the same misunderstanding.

What if you disagree?  You can say No, and explain why.

Read the comments with an open mind.  The reviewers are helping to improve your paper.

Revise to remove defensiveness.  You don't need to explain why you made a mistake, if you're going to correct it.

In what circumstances should you quote your text? Your goal is for the AE to make a decision without rereading you paper.  Many review comments don't give enough information for the AE to evaluate your change.

What about changes that were not requested?  Describe them if they would make a favorable impression.

Advice to authors, using anonymous examples

Feb 27:  Discussions (examples)

What needs to be accomplished in the Discussion?

Significance of the results

Comparison to other studies

Explain unexpected results

Evaluate uncertainty (or confidence) in the results, limitations of the study

Address the questions raised in the Introduction

Implications for management, other applications

Suggestions for future research

Conclusions (may be a separate section) 

Examples you brought


  1. decomposition: explain unexpected results (no differences)
  2. decomposition: other studies that found differences
  3. decomposition: other studies that found no differences
  4. C:N results (differences)
  5. interpretation and comparison to other studies
  6. ergosterol: interpretation and comparison to other studies
  7. intro to nematodes (absent from the Intro) and interpretation of results
  8. nematode communities, comparison to other studies
  9. conclusions.  length of the study could be a limitation, variability of genotypes
  10. need for future research 


  1. theory of emergy
  2. indicators of sustainability: proportion of sustainable inputs.  Interpretation and comparison to other studies
  3. same, different indicator of sustainability
  4. same, different indicator of sustainability

There are tables and figures in the Discussion, because they illustrate the interpretation of the results.

Section 4.2.

Components of emergy.  Interpretation.  Implications for policy.


Lacking:  comparisons to other studies


  1. Summary of results and conclusions
  2. Intro, results, interpretation, and application of dry mass measures
  3. comparison to other BIA studies, with useful criticisms
  4. comparison to other BIA studies.  Other studies promote it, they don't.
  5. comparison to FM results, interpretation, results of other studies
  6. effects of temperature.  Table for pros and cons of the methods, citing other studies
  7. Application of this method (consider biopsy)
  8. Summary and advice for sampling


Section headings are consistent with headings in the Results

Two of the section headings are their questions from their objectives.

Conclusions, why these questions are important

More like a review paper, though the first section focuses on their results 


Each paragraph restates the results and then compares them to other studies.


  1. Evalution of emission estimates
  2. Uncertainty in baseline ozone
  3. Comparison to modeling studies
  4. Temperature and climate change
  5.  Future study

53-55.  Summary (In conclusion).  Spring, Summer, Winter.

March 3:  Introductions (yours)

Allison: Am I telling the story in a logical order?

Amanda brought two.  The new one needs more help.

Sarah:  Order.  It seems short, what needs development?

Ying:  How to tell the story, from the broad picture to my project.

Gram:  I have the paragraphs that I need to write, but I don't have the full literature review.

Jackie:  Order.  How to give enough background that someone not in my field could understand it but providing enough detail to interest someone familiar with the topic.

Eugene:  Like Sarah and Gram, it's brief.  I have the main topics but I might need to clarify or add citations.

March 5: Discussions (yours)

Allison added a new experiment to her results, methods and intro--no discussion yes

Amanda: It's very fresh, so there are probably a lot of errors in it.

Sarah:  Mine is pretty rough, too.  It's the hardest section to write.

Jackie:  It's hard to organize because all my ideas interrelate.  Did I explain enough how I got from one concept to the next?
Ying had a combined results and discussion but tried separating them.  This was a helpful exercise.

Gram:  I tried separating the results and discussion

Eugene:  I didn't have time to finish it, it's a glorified outline now.  It's hard to know which things are important to explain.

March 17:  Feedback for Improvement


Gram: Quagmired in the discussion, need to resist chasing certain rabbits beyond the point that's relevant to the paper.  

Deadlines can help.

Eugene:  When looking for the sources of transformities, I found authors citing other sources.

Depending on how much work is involved, it could be a separate paper.  If so, don't do it now.

Depending on how much you care (does the conclusion depend on it?)

Jackie:  My co-author wants speculation in the discussion; some reviewers don't like it.

Ying:  I revised my introduction to focus on the subjects, not the authors.  I better developed the discussion about weather systems.  I want to keep writing but it's getting long.

Sarah:  Each of my sections was written independently and now I'm trying to make it flow as one story.  How all the pieces fit together.  The bread crumbs lead to the right place.

Amanda: Under time pressure, I'm not scrutinizing the literature as much as I should.

Eugene added a section explaining emergy analysis, after the introduction and before the methods.

Jackie has changed some questions and tried to link everything together.

  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, Background Presentations  3, 3, 5, 3, 5, 5  add a request for a cheat sheet or a model paper

Could the Intro be sequenced earlier to give background the class of reviewers?

Getting Started 5, 2, 5, 4 , 5, 5  forces clarity, very helpful

Choosing your Journal 4, 5, 3, 4, 2, 3

Figures and Tables 5, 4, 4, 4, 5, 4

Outline and Objectives 2, 3, 4, 2, 3, 3

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

Materials and Methods 5, 5, 5, 3, 5, 5

Writing exercise, in class 2, 4, 2, 3 ,2, 3

Preparation for peer review 4, 2, 2, 2, 3, 4

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

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

Statistical Considerations 2, 5, 2, 3, 2, 3

Responses to Reviews  4, 4, 2, 2, 4, 4

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

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

Getting feedback on our writing is what people find most useful 

  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.

3/19:  Readings on Peer Review  2, 1, 2, 2, 1, 2

3/24:  Ethics  3, 1, 2, 3, 2, 1

3/26:  Authorship 3, 1, 2, 3, 2, 1

3/31:  Proposals  3, 3, 4, 4, 4, 4

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

4/7:  Reviewer feedback and help session  5, 5, 5, 5, 5

4/9:  Writing exercise, in class  2, 3, 3, 3, 2, 3

4/14:  Abstracts (examples) 5, 5, 4, 4, 5, 4

4/16:  Work session  2, 5, 5, 3, 3, 5

4/21:  Abstracts (yours) 5, 5, 5, 3, 5, 5

4/23:  Steps to Publication  5, 5, 4, 5, 5, 4

4/28:  Last Class (Final Steps) 4, 5, 4  4, 4, 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 liked being in triples, so that two people can discuss your paper at the same time and piggy-back on each other's ideas for improvement.
  • It could be nice to discuss papers in groups of 3.  This way 2 people could bounce ideas off each other for the 3rd person's paper.
  • This has been the most helpful part of the class, it is great to have people mark up your drafts and give you ideas you wouldn't have thought of.
  • I don't find these too helpful, with varying backgrounds, I found that the comments to be generalized. Feedback was appreciated, but felt watered down.
  • I like discussions in groups of 3. It is more efficient to have suggestions when I can discuss with another reader.
  • I don't have a preference on whether we are in groups of two or groups of three, but I agree that reviewing in class and having time to discuss the comments with the reviewer directly is very useful.

Writing formal reviews out of class

  • I personally feel that writing formal reviews wastes time.  I'd prefer to spend that time thinking critically and writing on a person's actual paper, rather than typing up answers formally.
  • I liked the process of writing the formal review, but found writing the response to the reviews pretty tedious, especially since our drafts were still in a fairly early stage (so there might be drastic changes made before the next draft).
  • Reiterating what others have said, I found peer reviews to be somewhat of a time sink in the early stages of writing. That being said, it was helpful to critically assess how others have structured their papers and think about whether or not your paper contains the same strengths or weaknesses.
  • I actually found this to be very useful. Reading another person's paper closely and thinking critically about it helped me realize some of the weaknesses of my own writing, and having to write responses to my reviewers vastly improved my paper in my opinion.

Informal peer assistance outside of class

Group discussion

  • This has been useful to me because hearing other people's views on many topics has helped broaden my perspective.

Going around the table to equalize participation:

  • I liked having this time at the beginning of class to see how everyone was doing and to discuss any issues that multiple people were having.
  • That seems to work well at the beginning of class, and then we can split into small groups and work on an activity/share drafts
  • Kind of frustrating to be put on the spot at the beginning of a cycle, while on the other hand, equally frustrating to simply reiterate an already stated idea when at the end of a cycle. I didn't find these to be particularly helpful.
  • I like it as it forces me speak out. Otherwise, I will just keep silent.
  • This has helped me focus my efforts on the most important parts of my paper, at least for the purposes of this class. Very useful.

Class notes

  • Class notes are helpful - to have a record of our class discussions of certain sections that we can review while writing drafts.
  • I very much like the class notes for a reference of what has been discussed.
  • They are helpful. When I was writing my discussion, I looked through class notes to know what I could include in my paper


  • Food is always delicious and a great way for us to talk about our papers in a more informal setting.
  • I'm not too keen on potlucks.
  • I like food but I'm liable to forget to bring something unless I'm reminded somehow. 
  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?
  • I liked the diversity. I didn't think it presented many problems in peer reviewing.
  • I think it was good that we had the powerpoint presentations during the first class.  It'd be useful if everyone also included a handout of definitions/key information.  Then we could always refer to this information to remind us about papers that we read.
  • The diversity was great, it allows reviewers to pick up on things someone in the field might not. Obviously it would be nice to have very specific feedback on the subject, but we can get that in other places (advisor, lab group, co-authors, etc). Going over background information in the first class was really useful, and should definitely be done in future versions of the course.
  • It seems that a few of the students studied vastly different areas than others and were left to struggle with comments that don't pertain to their particular field.
  • It may be helpful if everyone can pick up a published paper and have others read it at the beginning. In this case, we will know what papers in other field look like.
  • I agree with the previous comment that having everyone read a paper in the field might be equally as important as giving presentations on our own work. That would be a lot of reading so maybe it could be something that's arranged over the semester break before the class begins if others think it'd be helpful. I find that people still don't really understand some of the main concepts of my work, but that has also strengthened my paper by forcing me to explain them better.

Select a paper that will help students from other disciplines understand your work.  Highlight the areas that caused you to select this paper, if possible.  

Cheat sheet: explain key terms, concepts, abbreviations, symbols.  ideas unfamiliar to a non-specialized audience.  Authors may benefit from this exercise.

  1.  Other comments or suggestions.
  • I think it would be helpful if we spent more time talking about specific issues we are facing as we write.  I think this could be accomplished by spending less class time reviewing each other's papers.  Instead, I think it would be beneficial if we e-mailed the specific section to 2 peer reviewers before class.  Then we could each come to class having already read and edited the sections.  This would allow us to spend a greater portion of the class period giving suggestions to each other about how to improve our papers.  We could even include questions/areas for the reviewers to focus on when we e-mail out the sections.  We could then discuss as a group specific problems we each had or items we noticed in each other's papers.  It could be a more productive brainstorm session at the beginning of class to address specific problems, rather than us each saying the difficulty we had in writing the section.   I don't think our revisions outside of class need to be formal reviews, but simply more in-depth corrections of each other's sections.  It's frustrating to only receive in-depth feedback twice.
  • Personally, I really enjoyed reading draft sections in class and getting feedback then and there. Any given section is short enough to read one or two during a class period, and those were the most valuable class sessions to me. I actually think that there could be more classes where reading over sections was done. Maybe in the next few weeks we can continue to read revised sections in class, separate from the formal review on the full drafts.
  • I heard from previous students that the semester culminates with our papers being sent to a scientist of our choosing for review.  It would be very helpful to have a researcher from my field offer me comments on my paper before I submit it to a journal.  If this is possible again this year, I would greatly appreciate it.
  • I think it might be interesting to break sections into different parts as we review them. For example, instead of reviewing the entire draft of an introduction in class, perhaps break it down over several sessions (sacrificing some of the sessions that are seen as less useful) and focus on individual components that make up a good introduction. Or, for discussions, pick an objective in your paper and focus a discussion around that. Fill in the discussion section gradually based on each objective/result instead of muscling your way through only to receive comments on rougher portions or having to redefine your entire approach. This could help with pacing and organization.
  • I enjoyed talking about issues we had at the beginning of the class. After we were broken into small groups, these issues were forgotten. I really like to have some feedback and good suggestion after discussion. Most of time we were just talking about problems in the draft. I hope I could get more suggestion for improvement.
  • Need input from someone in our field earlier in the process - perhaps have to present major professor with methods and results? that way large issues can be addressed early on.

You should get all the help you can from co-authors or anyone else who will listen.

March 19:  Second Draft

Gram has simplified his discussion of the ratio by referencing analyses by other people.

Eugene brought his new section describing emergy analysis.

Ying brought the time series of baseline CO2 and O3.

Sarah brought the discussion.  It's the most meaty section.  Does it make sense?

Amanda's MP asked her to report interactions over time, which changes the results.

Reviewer assignments

You will review the paper of the person after you in these lists:

Sarah - Eugene - Ying - Allison - Sarah

Gram - Jackie - Amanda - Gram

March 24: Ethics

Outlier: 139

It's important to scrutinize your data and have criteria for what's acceptable.  State the criteria for rejection if you reject any.  There are statistical criteria for outliers (but these are extreme).  You can try analyzing the data with and without suspicious values.

Conflicts of interest: 142 industrial, 144  competition

John will find out whether his professor is the sharing type.

Sandra will suffer if she can't publish her work.  She should have been involved in a negotiation up front.

ESF has a conflict about patenting the American Chestnut.  The plan was to make it freely available, but ESF needs money.

Allocation of credit: 145  

Ben could approach Freeman to give him the chance to apologize.  Check with the advisor, who may know what Freeman is like

Authorship (credit): (146,) 147,

Misconduct:  148, 149, 150

March 26:  Authorship

Author lists

Law, Diemont.  Diemont got 25 points on Galindo-Leal, on Dixon and Conner he got 2.  Marginal on both.  He got a grant to do the project, the Green Infrastructure people wanted the analysis (we don't know if it was his idea).  He hasn't had much input on it.  

Jackie has a project where she is working at one site and other people are contributing information from other sites.  I just collected the soil samples, why would you include me as an author.  

Gerson, Driscoll, Roy.  Possibly more if she gets more data from RIT or EPA.  Charley got lots of points because he's been involved all along and it was his idea.  Karen Roy didn't get very many points.  Charley's procedure is to include more people as it encourages cooperation.  

Zhou, Mao, and the person at EPA who suggested the project.  

Mount, Limburg, Schmidt.  They each got 40 points, in different ways.  For other papers, there will be an additional author, but he won't be on this one.  

Use your coauthors!  If this product is not going to earn you a degree, you can ask them to contribute to the writing, the data analysis, anything.  If this is supposed to be your project, then your co-authors may be functioning more like reviewers. 

Gray, Powell, Briggs.  The second paper will also have Horton.  Powell only got 15 points, but I need to include him; this was negotiated up front.  Briggs got 55 points.  Powell may start contributing more soon.

Allison knows that Maynard and Powell are on all the papers, at the end of the list, for providing funding.

Is it good or bad to be last author?  There are different conventions in different scientific cultures.  In Korea, last and corresponding author

Who is the corresponding author?  This person communicates with the journal through the publication process. If the lead author is not in a permanent position, the corresponding author might be a professor rather than a graduate student.  This is less of a problem now than it was before the electronic age.

When multiple papers are involved, you might assign authorship to fairly reflect contributions across the ensemble.  

Oakes, Desmarais, Powell, Maynard.  (The person whose lab it was in goes last.)  Tyler did all the data collection.  He was a new grad student.  

Is there a problem with delegating data collection (or other parts of the process?)

Some journals require that everyone on the author list verifies that they agreed to submission of the paper.  This can help when there are conflicts among the authors.

More and more journals are giving specifics of who contributed what on the author list.  


Allison will acknowledge undergrads who contributed to data collection.  

Jackie was included as an author for her undergraduate contributions to data collection.  Amanda had an undergraduate internship and she'll be included as an author.

Eugene's undergrads put in time but didn't understand the overall project.

Independent study is different from

Amanda:  undergrads, Andy Newhouse for the field management.  What about her boyfriend who is helping in the lab at Cornell?  In thesis acknowlegements people talk about relatives; in a journal article not so much.

Sarah had a lot of field help.  How many are appropriate to list?  I'll put them all in the thesis.  and everyone who helped in the field.

If you put their names in, send them the paper when it's published.

Ying will acknowledge her labmates for software and graphs.  

Jackie:  NYSERDA, ALSC, people in this class, my outside reviewer.  Lab manager, helpful people from the NERC meeting.

Eugene:  reviewers, two of the designers who helped with data sources.  The other people I interviewed, maybe collectively, not by name.  The funding agency.  Elliot Campbell talked to me after a presentation at a conference.  

Be specific, it gives more credit to the person acknowledged and it's more interesting to read.

Funding sources, data sources, agencies, reviewers, facilities.  Fellowships.  

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

March 24: Proposals

What's in a proposal

Introduction gives background necessary to understand the objectives, as in a paper.  The audience is likely to include people not expert in your field.  It's important to establish what has been done before (in a paper, some of this belongs in the Discussion).  In a 15-page proposal, there will be more space devoted to background than you would want in a journal articles.  

Objectives:  Might include predicted results and approaches.  Might include outreach, extension, broader impacts.  They may be categorized if there are more than 3.

Rationale and Significance   is required by some agencies.

Methods are almost like operating procedures.  More detailed than in a journal article. Address the choice of methods.  Preliminary results. Novelty of methods may be important.  Include plans for data analysis.  It can be a good ending to the project description to explain how the methods will achieve the objectives.  

Other endings:    Expected Products and Outcomes.  NSF ends with Broader Impacts.  Relevance to the mission of the agency.

Timetable: most often required for contract work (e.g. NYSERDA, EPA).

Program Evaluation is likely important in outreach and education.

Information about who's doing the work:   Research Team.  Current and Pending Support (C&P).  CVs (NSF Biosketch), commonly 2 pages.  Sometimes 1.  Conflicts of Interest (COI): collaborators from the last 5 years, thesis advisor and advisees.  

Budget, Budget Justification:   The justification is a place where you can show that you've thought through the details (and find them when you need them).

Spending the money differently than budgeted may need to be approved (for NSF, only if the change affects the indirect rate or international travel).

Letters of Support, supplying data, supplying access to sites, access to analytical services.

We also looked at RFPs (Requests for Proposals)

Eugene read an RFP for use of a computing facility.

Reviews of proposals:  Ranking E, VG, G, F, P.  Review comments.  They may be asked to review specific criteria.  Feasible

Advice:  Look at examples of successful proposals.  Get friendly review.  Enumerate objectives.  Don't state null hypotheses.   

April 2:  Peer Review (Readings)

Gender-bias in the refereeing process?

7 of 24 editors agreed to provide this information from their journals for a year.

There is bias, but it's not sexism.  The number of authors: Single-author papers are less likely to be accepted than papers with more than four authors.  Country of affiliation: better to be from a high-income English-speaking nation.  

The effects of blinding on the quality of peer review.

Each paper was sent to one review blind and one reviewer non-blind.  The authors and editors reviewed the reviews for quality.  The blinded reviews were better.  Quality of the review: importance of the question, strengths and weaknesses of methods, constructive suggestions on presentation.  Thoroughness, constructiveness, fairness, courteousness, and knowledge.

Effect on the quality of peer review of blinding and signing

Errors were introduced into a published paper and it was sent out for review.  Five treatments (blinding, signing, author affiliations, and control for being told they are in a study).  Blinded reviewers are less likely to recommend rejection.  The mean was finding 2 of the 8 problems.

Trial set to focus on peer review

A biotech company working on a protein with potential commercial applications.  One of the researchers submitted a paper to Nature which was reviewed by a researcher at a competing biotech firm.  The reviewer told the editor that the reported sequence was wrong, but he took the reported sequence and patented it.  In the patent is the mistake in the reported sequence.  The legal question is whether the review process is confidential or whether the material is public once you submit it.  Settled out of court for $21 million.

A case for instant peer review?

The peer review process takes too long and inhibits productivity.  Publishing flawed work would promote communication.  Reviewers are biased so the review process is unfair.

Discussion: publishing bad science can have serious consequences (measles in America)

Do readers and peer reviewers agree on manuscript quality?

The same papers were read by readers, reviewers, and experts.  The peer reviewers were not as critical as the experts.  Readers rated the rejected papers as more interesting.   

The philosophical basis of peer review and the suppression of innovation

Innovative ideas don't make it through the peer review process.  Quality control. Examples: 60 years to get a Nobel prize for work that didn't get further support at the time.  Ideas that got rejected but turned out to be right.  Advice to editors on choosing reviewers.  Be aware of conflicts of interest, corruption.

Peer review and the relevance of science

Evaluate effectiveness, efficiency, autonomy, accountability, responsiveness vs. inertia (resistance to new ideas), fairness, reliability, validity.

An examination of sources of peer-review bias

Authors submitting posters and others were asked to review other submitted posters.  Authors were more critical than non-authors.  Reviewers were not randomly selected.  Were all the reviewers better than average?  Maybe.

Peer review practices of psychological journals:  The fate of published articles submitted again.

12 published papers were submitted to the journals that published them.  They changed the names and authors of the institutions.  Only 3 of 38 editors and reviewers noticed this trick.  8 of the 9 papers were rejected.  Grounds for rejection were serious methodological errors (not a lack of novelty).  100 pages of responses published in a special issue.

Gunning's Fog Index:  Number of words per sentence, percentage of big words (more than 3 syllables).

Drawbacks of peer review

One published paper was sent to 45 experts.  Results were highly variable.

Nepotism and sexism in peer review

Friendship bonus --reviewers are easier on authors who are connected to them.  Blinding would help, hard in a hiring process. 

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

286 reviewers were surveyed:  2-4 hours per paper (45 minutes - 8 hours),

uncompensated labor.

April 6: Publication Productivity (readings)

Is productivity always measured by publications?  

Gender, life course, publication decisions, in toxic-exposure epidemiology

Age, rank, seniority.  Where to publish first, with material that might be controversial.  Is self-confidence lower in women?  This affects selection of a journal and of research topics.  Semi-formal interviews of 70 people.  Gram thought this was too subjective, then they do statistics on it.  Women progress more slowly through the ranks.  

Child care, research collaboration and gender differences in scientific productivity.

Norway.  Surveys of professors in a variety of disciplines.  252 women, >1000 men.  Women with children under the age of 6 are less productive.  It evens out after the kids are 10.  Are women excluded from research networks?  Women not in networks are less productive, more so than men.  1996.

Gender, family characteristics, and publication productivity among scientists (Fox)

Women with small children are more productive than women without children or with school-aged children.  631 men, 178 women.  biological and physical sciences.  1994

Cumulative disadvantages in the careers of women ecologists

  1.  This field was dominated by men.  Need an update: are women dominant yet?

Men publish more and have higher salaries.  They surveyed everyone who participated in a graduate program (OTS) in the 1960s.  105 women, 229 men.  Analyze by age group, family situation (married, single, with and without children).  The only ones unemployed (3) were women.  Most working in government positions were men.  Women took more temporary positions and had lower job security.  

Publication productivity among scientists:  A critical review (Fox, 1983)

Psychological characteristics: autonomy, independence, self-sufficiency at a young age.

Creative and productive scientists are socially detached at attached to their studies.

Productivity peaks in 30s-40s, maybe again towards retirement (spurt obsolescence).  Movement into administrative roles, lose motivation, or get outdated.

Environmental location:  where you were trained matters more than where you end up?  

Organizational freedom is correlated with productivity.  Collaboration within departments.

Publish or Perish?  An author analysis of communication journals

Rank:  Full professors> Assistant > Associate.  More men than women in each category.

People from certain institutions publish in certain journals.

Gender:  ratio of papers by women is increasing.  

More women are getting PhDs than men.  2005.


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).

April 9 Abstracts (examples)

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

Progress reports

Allison has had and expects zero input from her coauthors.

Amanda calculated content and it's going in her capstone on Monday!

Sarah got tons of feedback, now from her advisor as well.

Jackie:  still waiting for coauthor, our review

Ying just got Eugene's review, which will help.

Eugene is working on the appendices, formatting from the database which he didn't set up they way people will expect.

Analysis of Abstracts

Gripping problem statement

Background information

(Methods if important, innovative, or unusual)



Conclusion, why the results mattered.  Implications for policy, management, or future study.

equal time for what's in your paper?

readers know where to go for what they're interested in


Boring background, good problem, objectives (experimental design and approach), more methods, results (6 sentences), conclusion disappointing, we knew that before we read the paper.  Results were the best part.


Boring background, objectives, methods, results (3 sentences), conclusion disappointing.  Why is this important?  To whom does it matter?


No problem statement.  Objectives, methods, then all results.  

Don't say something is discussed, consideration is given, are examined. Tell us the answer.


No problem statement.  Objectives, results, interpretation, conclusion.  Missing why this is important.


Gripping problem statement (3 sentences).  Paragraph break! Methods, objectives, results (3), summary, conclusion.  Tells us where this is applicable.


No problem statement.  Objectives with methods, results, conclusion.  Could have put it in the context of a larger problem statement.


No problem statement.  Objective (methods).  Conclusion.  Good problem at the end.

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

Literature citation

Amanda tried using RefWorks, it was hard to use, unusual characters don't come through.  So she redid it by hand.  SB&B provides software?

Sarah does it by hand.  So does Eugene.

Allison loves Zotero.  It's an add-on in Firefox, you click on the paper and it fills in automatically.  You have to check it, somtimes for capitalization.  Use it in Word, click and it inserts the citation.  Click to build a bibliography, using the format required by the journal.  

Jackie uses Mendeley, which is good for organizing notes and saving articles.  She exports to Zotero, maybe there is a way to generate reference lists directly.

Ying uses RefWorks and it works for her.  It includes the format for the journal that she wants.

Software prevents errors in the citation list and it makes it easier to reformat.

What order should you cite papers in?  Chronological.  Oldest to newest.

Place the citations as close as possible to the point of reference.

How to choose which papers to cite?  Most relevant to your claim in the context of your paper.  The original one?  The classic one that people will recognize.  Name-dropping.

A review article can be efficient.  Recent papers may cover the earlier papers.

We don't care where you happened to read something.

Cite good papers, don't cite bad papers.  Frequency of citation might indicate this.

You hope that you're not overlooking work by your reviewers.

April 14: Abstracts

Amanda just noticed that she still has Sr.  Will excise.  How much to say about methods?

Sarah is up against a word limit.  What could she cut to add a broader conclusion?

Ying has a list of results but lacks a general conclusion.  She didn't count the words yet.

Eugene: 250 words is not a lot.  I'm trying to say more with fewer words, and it may be too general.  Would it be better to say fewer things with more detail?

Gram:  I have too much, I'm over the word limit, but it still seems vague.

Jackie:  50 words over and no specifics.  I wanted to include implications.

April 16:  Help with Revisions

Status: How's it going?

Amanda brought the results.  How to talk about statistics for main effects and interactions.

Ying brought a section of her results that she revised to address more general issues instead of just the extreme events.

Eugene finally sent his paper to his co-author, who asked for it.  He is still working on the discussion and the appendices.

Gram reworked his abstract based on everyone's comments and now he feels something is missing; previously he had too much.

Jackie brought the results, she wants help with the figures, and how to show positive and negative trends.  She added a conceptual model.

People who want another review:

April 21: Intro to Zotera

Firefox plugin download:

Word Processor plugin download:

Style repository:

Thanks, Allison!

Jackie sent a Chrome plug-in 

April 23: Titles, Electronic Submission of Manuscripts

Status reports

Allison is still hounding co-authors for input.  Say, I plan to submit this on  If you need more time let me know.

Sarah is working on revisions, and she has heard back from two authors, the third will look at it later.

Amada is still making revisions, she's reformatting the results, then she'll work on the discussion.  

Gram is still looking into statistical analyses.  Make a consulting appointment.

Ying's advisor is looking at it again.

Jackie is working on the results and discussion to make it more meaningful.  Her advisor is still promising to get to it.

Eugene has been working on other things because this one is not time-sensitive.  His advisor is promising to work on it.

April 28:  Steps to Publication

Electronic submission of manuscripts

Final Drafts  

Allison: Thursday.  Considering whether to write another paper on humic acid.  This paper will justify the next paper.

Amanda:  There is one more set of samples.  It's nice to include it because otherwise they wouldn't be publishable.  Co-author will read it on Thursday.  Might be done by Friday night.

Sarah:  Could be done in a couple of days.  Wants to get more feedback from her lab group.  Not expecting big changes.

Jackie is still waiting for her co-author, and there's no telling how major the revisions will be.

Eugene's co-author keeps promising to get back to him.  He may want to add a lot to it.  The grant was for a social sustainability analysis as well as an emergy analysis. Another professor and student did the social sustainability analysis and Eugene doesn't want to write it up for him.

Papers.... are going to trickle in prior to May 1st? So the 30th. I can have mine in on the 28th. But most on the 1st.

We determined a priority scale for grading:

High priority: Amanda (defending in July)

Medium priority: Eugene, Ying, Sarah, Jackie

Low priority: Allison, Graham (trapped here forever)