FOR 694 Writing for Scientific Publication

Ruth Yanai,  210 Marshall,  x6955,  rdyanai@syr.edu https://www.esf.edu/faculty/yanai/

Spring 2017 Class Notes                   

Date

Class

Assignments Due

Jan 18

Why Publish?

Background presentation (5 minutes)

Jan 19

Discuss Getting Started

Getting Started Exercise

Jan 23

Choosing your Journal

Knowing your Journal Exercise

Jan 25

Figures and Tables Maddy,Yang, Alex, Autumn

n copies of Tables and Figures and captions

Jan 30

Figures and Tables Zainab, everyone else

n copies of Tables and Figures

Feb 1 Outline and Objectives Two copies of your Outline and Objectives with Abstract (revised)

Feb 6

Results

Draft of Results (two copies)

Feb 8

Materials and Methods

Draft of Methods (two copies)

Feb 13

Authorship

Authorship Exercise

Feb 15

 

Preparation for peer review

Editing and proofreading

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

Feb 20

Introductions

Bring 1 example from your field, n copies, number the paragraphs

Feb 22

Writing exercise, in class

Bring a difficult section

Feb 27

Advice, Responses to Reviews

First Peer Review Due

Mar 1

Discussions

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

Mar 6

Progress on Introductions (shared in class)

2 copies double-spaced

Mar 8

Progress on Discussions

2 copies double-spaced

 

Mar 13-17 (spring break)

 

Mar 20

Mid-semester feedback

Anonymous feedback

Mar 22

Readings on Peer Review

Submit  Rough Draft and Response to First Reviews

Mar 27

Ethics

 

Mar 29

No class

Catch up!

Apr 3

Proposals

Bring examples of RFPs, proposals

Apr 5

Readings on Publication Productivity

Second Peer Review Due

Apr 10

Reviewer feedback and help session

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

Apr 12

Abstracts

 

Apr 17

Help with revisions

Bring n copies of an example from your field

Apr 19

Statistical Considerations

Bring your questions

Apr 24

Abstract review

Title, by-line, key words

2 copies double-spaced

Apr 26

Steps to Publication

 

May 1

Last Class (Final Steps)

Final Draft of Manuscript and Response to Second Reviews

Outline and Objectives

Jan 18:  Why Publish?

Presentations

https://drive.google.com/drive/folders/0BxXuVrpNGuD9U1pwQVZhdnJRamM

Yige Yang was in a candidacy exam!

Maddy Morley, Sophomore in EFB.  Snapchat.  N and P additions, effects on leaf retention during fall senescence.  Birch dropped leaves earlier if treated with N.  Maple didn't care.

 Dan Hong: Regeneration of sugar maple threatened by beech sprouting, due to beech bark disease.  Maple is a valuable timber species.  26 stands in the White Mountains of New Hampshire.  No effects of N or P treatment on regeneration (stem taller than 50 cm but < 2 cm in diameter).  Effects of overstory trees, effects of stand age.

Alex Young: Tardigrades:  Do they care where they live?  They can survive 20 years without water.  Vertical profile in a canopy, different epiphytes (hypogymnia lichens, bryophytes, allextorioids).  Climb trees, collect epiphytes, observe under a microscope, tardigrades, rotifers, and nematodes. 

Autumn: biogas production from anaerobic digestion of office paper.  Steps:  hydroloysis, acidogenesis, acetogynesis, methanogenesis.  Cow manure have the microbes needed for inoculation.  Office paper contains cellulose and other carbon. Different combinations of manure, paper, and temperature (and water, 94% water). 

Jeff (2nd year PhD in ERE):  remote sensing to analyze riparian vegetation, which is important but difficult to monitor.  Objectives: high resolution, trend analysis.  Genesee River Watershed, listed as impaired, discharges into Lake Ontario, riparian vegetation compromised.  2008 to 2015.  Riparian Vegetation Index (RVI) varies seasonally, but also declines over time.  Lack of riparian vegetation leads to more changes in channel morphology (agricultural fields).

Yang Yang (PhD, a graduate of this class):  Mercury (elemental, gaseous, particulate), taken into trees through leaves and roots.  Four sites, Huntington Forest (NY), Sleepers River (VT), Hubbard Brook (NH), Bear Brook (ME), hardwood and conifer trees,

Zainab Tariq (GPES Ecosystem Restoration, MS thesis research): Biodiesel production from bitter almond oil, a non-edible feedstock, compared with fresh vegetable oil (FVO) and waste vegetable oil (WVO).  Physico-chemical properties.  Alkaline transesterification: glyceride + alcohol → esters + glycerol.  Find the optimal ratio of alkali (KOH, NaOH).  Bitter almond grows on marginal land, semi-arid and arid climates.  Production was banned in 1995. !?

Why Publish?

Autumn:  I want to go for my PhD and an academic, you need a publication record.

Maddy:  It would be cool to get my idea out there.

Dan:  There is a big data set, since 1994, a lot of people put work into it, and there should be a product at the end.

Alex:  Facilitate conversations between the moss and tardigrade communities.  Promote interdisciplinary transfer of ideas.

Yang: To get my name out there.  Make connections, gain collaborators.

Zainab:  I did this work in 2011, and I haven't been in touch with this field.  I will catch up on the last 6 years of research.

Jeff: This is the methods paper, it needs to be published before the next paper.

Autumn:  Bragging rights.  I will be the first to publish in my family.

Maddy:  I want to be a first-author sophomore.

Alex: To document the current situation, for future reference.

Jeff:  I had a bad experience, it took 5 years to publish my MS thesis.  I want to have a better experience this time.

Intro to Getting Started

 

Jan 19: Getting Started Exercise

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

Autumn:  It took me four or five tries until I got it down to size and rearranged it.  I'm still finishing my experiment but that wasn't even the hardest part.

Ruth:  It's quicker than writing a paper.  It's a good way to feel out whether you should write two papers or one, for example.

Dan:  Like Autumn, I don't have all my results.  It was hard to prioritize the ones I have.  The order of presentation of the results is important.  The results are not very interesting and not expected.

Maddy:  Trying to be precise takes longer than 10 minutes.  I have to decide whether the method or the result is more important.

Yang:  I have clear objectives and results, but the problem statement is not that impressive.

Zainab:  When you start your study you have clear objectives but it's hard to show how your results stand out from what else has been done.

Dan:  Mine got simpler but less interesting.

Alex:  I had trouble figuring out which theoretical constructs are relevant.  Do I leave out the parts that aren't interesting?  I have more detail on tardigrades than the other groups.

Ruth:  Intro and Discussion are harder than Methods and Results.

Autumn:  If I gave myself only 10 minutes it would have been better earlier.

Jan 23: Choosing your Journal

Factors to Consider

Where similar work has been published in the past, particularly by her co-authors.

Aims and scope: Elsevier has a tool that will examine your abstract and suggest which of their journals you should consider.

Impact factor, on the journal website.  Number of citations divided by the number of papers over some time period.  2.8 Forest Ecology and Management, 1.7 Canadian Journal of Forest Research, 1.7 Forest Science, 1.0 Bryologist, Forest Ecosystems 3.75, Ecosphere 2.3, Building and Environment 3.4, J Hydrology 3.0, J Great Lakes Research 1.9, Ecological Indicators 3.2, Remote Sensing of the Environment 5.8, J Renewable and Sustainable Energy 1.0, Bioresources 1.3, Advances in Applied Science Research 0.3, Science of the Total Environment 4.0, Environmental Science and Technology 5.4

Speed of publication: Some journals have graphs showing their turnaround time over time.  Check whether your paper will be available on line upon acceptance.

What are the time lags?  When you submit it, it gets assigned to an Associate Editor, who solicits reviews, then reviewers review it, then the AE makes a decision and sends it to the author with a request for revision, usually with a timeline, and then it could go out for review again.

Costs range from free to $100/page for Forestry Chronicle, $65 or $85 for members or non-members for Pacific Northwest Science.  Some charge for color figures – check whether they charge for color in the pdf.  $105/page for Bioresources Journal

Open Access: Free to readers. $3000 for Ecological Indicators, Ecology, $3600 for Forest Ecology and Management, $2200 for J of Renewable and Sustainable Energy,

Check to make sure there is a source for the funds if you're going to pay for publication.  It's possible for our Research Office to pay publication costs for projects that no longer have funding.

Acceptance rate.  Not all journals make this information available.  You can write to ask for it if they don't have it on the web site.  32% Science of the Total Environment, 65% Journal of Great Lakes Research IF=1.9, Ecological Indicators 44%, 3.19,  Remote Sensing of the Environment 29% 5.8, 21% for Building and Environment IF 3.4,

International audience, don't be fooled by the title.  Check the scope and impact..

Journals you chose

Yang:  Science of the Total Environment:  relevance

Autumn:  J of Renewable and Sustainable Energy:  my co-author publishes there.  Free or pay for Open Access

Ge: Ecological Indicators:  Impact Factor, Acceptance Rate, and Audience

Yige: Building and Environment: major journal for green roof performance and design.

Maddy:  Forest Ecology and Management:  IF factor, turnaround, audience of managers and policymakers

Alex: Opuscula Philolichenum: free and recommended by a collaborator.  IF 1.04.

Dan:  Forest Ecology and Management:  relevance

Read the instructions

Length of the text:  unlimited, 20 pp, Zootaxa defines notes as <6 pp., figures may or may not be included in the page count. 4,000-8,000 words, 7,000-10,000 words

Length of the abstract, <200 words, 200-400 words, <400 words,

Number of figures or tables, not mentioned, keep minimum, require only high quality image, 300 dpi, tables type-setting, no more than 15 figures.

Page charges.

Required sections (must results be separated from discussion?  Is there a separate conclusions or summary section? Forest ecology and management requires a section of management and policy implications. Funding or conflict interest to be separate section.

References:  50,

 

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.

Specify the meaning of your error bars (SD, SE, CI)

Site names:  Don't ask your readers to memorize the meaning of your site names (don't ask them to learn any unnecessary vocabulary

Mean and SD

Consider using color, if it won't cost you more.  Use colors that can be distinguished in black and white.

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

How many digits are meaningful to report?  Precision of the measurement.  Enough digits to see differences (e.g. isotope ratios).  Use the s.e. of the mean to judge the precision of the mean.  One digit of the s.e. is probably enough.

Align numbers on the decimal

In a table, put the reference (if any) on the right hand side.

Font sizes (bigger)

A diagram may be better than a photos of your experimental setup.  Try Manga, Paint.net (for free), or Powerpoint.

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

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.

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

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)

Feb 1: Outline, Objectives

 

Ge:  Because it's a methods paper, some of the results about the effectiveness of the method could be in the Discussion instead of the Results.  It seems better in the Results.

Yang:  usually I write an outline only for the Introduction and Discussion, because the organization of the Methods and Results is more straightforward.

Maddy:  This is cool.  It looks so legitimate (in the template I provided).  I will need to dive into the lit review.  Some things won't become clear until after I do that reading.

Alex:  I had already written the Introduction and the Methods.  So I had to look at my topic sentences and what order I was bringing things up in.  I had rearranged things a bunch of times.  In the Results, I'm wondering how to talk about different significant differences across my different classifications.

Zainab:  I used the Purdue University model, which helped me identify how I need to put my work in the context of what has been done.  It raised questions that I hadn't been thinking about when I was doing the work.  Suggesting future work.

They suggest we restate the objectives at the end of the paper.

Yige: It made me go back to the instructions to authors from the journal.  They require highlights.  Writing the outline made me think that I want to focus the paper on the relationship of the physical properties to the performance of the green roof, not the methods for characterizing them.

Dan:  I struggled the most with how to start.  How general should my first paragraph be?  Some papers start with what they are doing and others start out big.

Autumn:  I didn't do it all in one sitting so it might have redundancies.  Do I need a site description?  Not necessarily.

Feb 6:  Results

What do you want help with?
Alex:  Using statistical programs that I don't understand (ggplot2 in R).  Table columns, take a look.
Yige:  I feel so stressed.  I don't know how to start.  It's not the same as writing a lab report.  The style of a journal report is different.  I realized that I need to do some additional statistical analyses.  Sometimes I don't know whether material belongs in the Results or Discussion.  I need to do more literature review.
Zainab:  Sometimes it's hard to be selective.  I have to decide which results from my MS thesis belong in this paper.  It's hard to decide how much of the methods to describe in the Results.  I wonder if the pictures are worth including, when the results are presented in figures and tables.
Dan: Like Yige, I'm concerned about what belongs in my Results vs. Discussion.  What alpha level should I use?  (Maybe you don't need one.  Report your P values.)
Maddy:  My results are short.  I'm not too confident with my technical writing.
Yang:  I need more time to do the stats.  Making the graphs is easy, but making the statistics takes more time.
Autumn:  Same.  I don't know whether the maximum production is significantly different yet.  When I add paper, I need to test whether the improvement is significant.  I read advice about not including discussion with my results (Gladon et al. 2011). 
Ruth:  Make sure the results are meaningful (unless you are a geologist).  Pose your questions in the Introduction and tell us the answers in the Results.
Ge:  Mine is a methods paper, so does the comparison of methods go in the Results, or the Discussion?
Autumn, Maddy, Dan:  I don't have all of my results yet.

Feb 8:  Methods

Yang:  No problems.

Dan:  Describing the statistical method was hard.  I haven't decided which method to use.

Alex:  How much detail is needed in describing the statistical approach?  Answer:  Just enough to replicate the study (by a competent analyst).

Zainab:  Like Dan, I haven't decided which method to use.  When modifying a method, how much detail is necessary?

Yige:  I decided not to describe the statistical methods in the Methods section.  The papers I saw in my journal didn't include them.

Maddy:  I have a lot of ideas, and I'm not good at wording them and structuring them.  I'm not sure how much detail to include.

Ge:  Like Zainab, I need to compare my approach to previous methods.  How much of this belongs in the Discussion.

Autumn:  I feel like this section is really long.  Did I say too many things, or do I need all of this.  I have a table of model parameters that is described in the text.

Feb 13:  Authorship

Author lists

Yang:  Yang, Yanai, Montesdeoca, Driscoll.   Points: 

Ge:  Pu, Quackenbush.  Points:  100, 45. 

Dan:  Hong, Wild, Yanai.  Points in Galindo-Leal:  60, 20, 45, but the scores will likely go up as people contribute.

What determines the order? 

  1.  Could be descending order of contribution.
  2. Alphabetical
  3. Last place is sometimes the head of the lab or the person who wrote the grant.

Who is the corresponding author?  One of the authors may have contact information on the paper.  The journal communicates primarily with one person, the corresponding author.

In China and Korea, the last and corresponding author gets as much credit as the first author.

Alex:  The senior contributor wants to be in last place. 

Dan:  What about chronological? 

How is conception different from design?  In some casesi

Autumn:  Elniski (executing and writing), Chatterjee (interpretation), Mondal (planning), and Doelle.  70, 40, 35, 20.  Doelle is the MP and will expect to be included.  He heads the lab.  Check whether Chatterjee prefers to be last, since he contributed more.

Zainab:  Tariq and Syed Shahid.  90, 60.  My co-supervisor got 20 points.  Hunt had a system for intellectual input that is more suitable for my field than the Ecology one.

For journals that list two authors in the text when a paper is cited, but only the first and "et al." if there are three or more, be aware that your second author is losing visibility when you add a third author.

Yige:  Yang and Davidson.  90, 40.

Alex:  Young, Miller, Villella, Carey, Nelson, and Miller (two different Millers).  17, 4, 5, 3, 1, 6.  Or 90, 30, 40, 15, 5, 30.  Do the 15 and the 5 belong in the author list?  Maybe not the 5, he just helped one day and wasn't much help.  The 15 climbed half of the trees and helped with the lab work and housed us.  Add a category for housing and he'll make it.  What about the order?  The 30-point person is a post-doc and he will benefit more from being second. 

Maddy:  For Snapchat:  Morley, Wild, and Yanai.  90, 80, 65 

For litterfall phenology:  Morley, Walsh, Yanai, Fisk  65, 60, 55, 25 

Yang:  Yang, Yanai, Driscoll, Montesdeoca.  90, 72, 65, 55.  Ask Charley if he prefers to be last.

Acknowledgments

Ge: The funding source, people who helped with data analysis.

Dan:  Matt Vadeboncoeur and Shinjini Goswami.

Autumn:  William Burry got points for contributing equipment.

Zainab:  The institute, organizations that provided technical assistants, instruments, reagents, and people who helped with interpretation and discussion.  Reviewers of the thesis.

Yige, the person who designed the device and the undergraduate who helped classify the rain storms.  Onondaga County.provided the green roof. 

Maddy:  Nera and Dwight for field work, Colin for SAS.

Maddy:  The people who helped with litter collection, plus Adam, Nat, and Alex.  What about all the people who helped sort litter?

Yang: The people who provided the field sites, people who helped in the field.  People who helped in the lab.  The funding source.  Hubbard Brook.

Alex:  The place where we collected, and this class!

 

1.  Use the point system described by Carlos Galindo-Leal in Ecology 101 (Bulletin of the Ecological Society of America, October 1996).  Make a column for each of the possible authors of your paper, and assign points for your various contributions.  Include yourself!

 

Planning

 

Executing

 

Analyzing

 

Interpreting

 

Writing

 

2.  Do the five categories of contributions suggested by Galindo-Leal seem appropriate for your project?  If you prefer, try applying a point system with different categories, such as those suggested by Hunt or Dickson and Conner.

3.  Name your authors, in the order you propose to list them on your publication.

4.  Does your list agree with any objective point system?  If not, what were the other factors that influenced your decision?

 5.  Who will you list in your Acknowledgements section?

Updates

Alex should be ready for Wednesday.  What changed the most?  My results.  Choosing what figures to include.

Yige:  Added two sections to the results, a regression analysis for hydrological performance.

Dan added simple regression graphs for different size classes of trees.  Yang is going to help you with statistics on treatment effects.  Started working on the Introduction.

Ge revised the Methods and Results and is working on the Discussion.

Yang was working on two other papers.  One is submitted!

Maddy:  It's getting cleaned up, it's been slow going.  I'm working on it. 

Zainab is still working on her Methods and Results, to distinguish them from each other.

Autumn: 

 

Please ask your reviewer whether they want your paper on paper or electronically.

Email them to me, I will review them in the order received.

Feb 15: Peer Review

Reviewer Assignments

Maddy reviews Alex reviews Yang reviews Maddy. 

Dan reviews Autumn reviews Zainab reviews Dan.

Yige and Ge 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

 

February 20: Introductions

What needs to be accomplished in an Introduction?

Literature review as needed to justify the importance of your work

Enough background to understand your paper

Previous work relevant to this topic, to pose your question

Problem to be solved, what is known and not known

Theory if necessary

Objectives

 

Examples you brought

Dan

  1. Background (too general, could have skipped this)
  2. Background:  maple and beech
  3. Problem, Objectives and Hypotheses, related studies

Ge

  1. Background: why riparian zones are important
  2. Background:
  3. Review of methods
  4. Background, problem statement, objectives.  The topics of linear vs. non-linear techniques and optimal spatial scale

Yang

  1. Importance of Hg
  2. Previous work on Hg in trees: importance of vegetation type
  3. Objectives and study description

No problem statement

Yige

  1.  Broad background on buildings and energy, why green roofs.
  2. Background on benefits of green roofs
  3. Background on benefits of green roofs
  4. Background on benefits of green roofs
  5. Background on benefits of green roofs
  6. Previous work, gap in knowledge, beginning of objectives
  7. Sounds like methods.  This was not IMRD paper.

Autumn

  1. Background (without importance)
  2. Background on theoretical models, problem statement (parameters are hard to estimate)
  3. Objectives are in the first and last sentences, and in between is a description of the study system and method.

Maddy

  1. Background: climate warming and leaf senescence
  2. Importance of growing season length, but respiration may counteract this.
  3. Background on leaf out, but leaf fall is less well understood.
  4. Knowledge gap, we need to achieve these objectives.
  5. Objectives, including study system, no other surprises

Zainab

  1. Importance of energy, alternative energy, biodiesel
  2. Background on biodiesel
  3. Background on the process, with a figure for the reaction
  4. Background, previous studies, problem:  cost and quality,
  5. Objectives, what but not why.

Alex

  1.  Problem: lack of information on tardigrades
  2. Problem: lack of information from Pennsylvania
  3. Introduces habitat preference
  4. Still habitat
  5. Habitat
  6. Habitat
  7. Objectives,

Flags:  "little is known", "only a few of the small number of studies", "further studies are needed," "poorly documented"...

Feb 22:  Writing

Zainab:  It's the most difficult part.  To compose your ideas, gather your thoughts, and put them into words.  It's easier in Hindi.  I have to think more about selecting words.

Yige:  It's hard.  I really like writing in Chinese.  I'm pretty good at writing in Chinese.  Even though it's hard, I like it because it helps me refine my ideas and organize my thoughts.

Autumn:  I enjoy writing a lot.  For the most part, I'm good at it.  The most issues I have are writing concisely.

Ge:  I actually love writing, ever since I read a book about how to write.  Now I find I write too much.  I need to condense my thoughts.

Alex:  I prefer speaking to writing.  I can organize things in my head, and I have a harder time doing that on paper.  I have a hard time knowing how much or how little information is needed.

Dan:  I like writing.  I have a similar problem making it concise and staying on topic.

Maddy:  I don't like it.  I have it in my head, but I have trouble structuring  it and putting it on paper.

Yang:  I like to start, but revising is painful.  I'm excited when I start and it goes fast.

 

Suggestions?  Try dictating.  Outlining.  Retroactive rescue outlines.  Come back to it later.  Know your audience.

Smith and Brown

Why did you like Smith better? 

Paragraphs are helpful.  Use topic sentences.

Shorter is better.

Directional signals:  "First," "second," "third."

The sentences are shorter and more direct.

Use the subject and verb of the sentence to carry the main meaning.

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

Loans

Zainab  Sentence skills, Brief English Handbook.

Maddy: Josh Schimel, Elements of Grammar

Alex: Elements of Style

Yang: Practical English Handbook

Dan:  Mike Kelly's book

Ge's recommendation:  10 days to overcome writers block

Feb 27: Reviews, Responses to Reviews

Thoughts on the review process

Ge:  It was very interesting, in a good way.  Yige's paper's field is what my undergrad was about.

Yang:  I have to go back and forth between the document and my review.  It's not like you can read the paper and then write the review in one sitting.

Maddy:  It took me a long time, I wanted to be very thorough.  I had to organize my own comments.

Autumn:  It took me longer than I thought it would, 3.5 hours for a 10-page paper.  I wrote on the paper as I was reading it.  I had more small comments (grammar, formatting) than major issues

Dan:  It took me longer because I don't know the subject area. I liked learning about it. It's different from reading a paper to get the main points. Every time I read it, I learned something new.

Yige:  I liked the topic, I have some background in the area.  I focused on the logical parts and the big picture.  Identifying which parts are overlapping and which are necessary.

Alex:  I read it once for general form and shape and a second time in excruciating detail, identifying problems. 

Autumn:  An advantage of marking it up electronically is that you can remove comments that turn out not to be relevant.

Zainab:  It's nice to be able to tweak the comments.  The topic wasn't in my area of study but I was able to understand it.  It was a good experience to put myself in the reviewer's shoes.

Ge:  I tried to make suggestions about the Discussion.

Autumn:  It will make me a better writer next time.  I know what to watch out for.

Dan:  It's easier to see other people's mistakes than my own mistakes.

How to write a response to reviews

Address your response to the Editor. 

Your goal is for the Editor to decide to accept your paper without sending it back to the reviewers.

Start by thanking the Editor, explain that you are submitting a revised manuscript, reference the manuscript number.

You won't need to provide the date or your name, if submitting electronically.

If there are important changes not motivated by the review comments, document them up top.  For example, changing the author list.  Doubling the sample size.  Changing the title of the paper.

Instructions for how to read your document:  Changes are in blue, or bold, or italics.  Responses are detailed below. 

When you get reviews from the journal, they will all be in one document.  Please combine your two sets of review comments and provide me (the Associate Editor) a single response document.

Retain all of the original reviews, responding to each point.

If you get opposite opinions from two reviewers, you have a reason not to comply with the one you don't agree with.

If the complaint is not clear, quote the necessary text to give the AE the background necessary to decide that you responded adequately.  "The statement in question is:"

Quote added text.

Don't be defensive.  Proofread and remove explanations for why you did something wrong and you are fixing it.

Defend yourself if you are not making a change.

You have to decide whether to make the change or not.

If the reviewer was wrong, see if there is something you can change so that other readers don't make the same mistake. 

Try not to have a string of suggestions where you did nothing.

Make it clear if you didn't make a change. "No change."

You may want to look at multiple reviewers' comments on a single section.

Start at the bottom if you don't want to affect the line numbers for sections you haven't revised yet.

Advice to authors, using anonymous examples

Less sugar maple saplings were present under overstory beech.

Each plot is 30m x 30m surrounded by a 10m buffer.

To describe the processing rate of Hg from each tissue type, we used annual net production rate (g m-2) for each tissue type and species at HBEF (Whittaker et a., 1974) multiplied by the concentration of Hg (ng g-1) of each tissue type at HBEF in this study.

Figure 3 shows that biodiesel yield and the conversion efficiency was maximum at 5:1 molar ratio (84.33 - 2.96) % as compared to 7:1 (78.19 - 5.99) %, and 9:1 molar ratio (63.33 - 7.69) % among all biodiesel samples.

Land cover in the area is dominated by agriculture (52%) and forest (40%), with smaller amounts of developed land (4.6%), including a mixture of residential, commercial, industrial, and transportation/utilities uses, wetlands and water (2%), and other non-developed lands (1.4%) (Makarewicz et al. 2015).

At all four sites, soils are well drained Spodosols developed in glacial drift (Somers 1986; Huntington et al., 1988; citation).

Despite their cryptic nature and diminutive size these organisms participate in ecosystem services such as forming critical components of canopy food webs and playing a role in canopy nutrient cycling and epiphyte reproduction (Lowman & Rickner 2004; Rosenstiel et al. 2012).

March 1:  Discussions (examples)

What needs to be accomplished in the Discussion?

Interpretation of the results--gray area.  We want the results to be meaningful. 

Minimizing space devoted to recapping your results.

Explain unexpected results.

Comparison to other studies.

Importance!  Novelty.

Limitations of the methods and how they affect the results

Implications (Recommendations) for policy, management, commercialization, conservation.

Directions for future studies.

Conclusion

 

Examples you brought

Autumn

  1. Comparison to other studies, interpretation (paragraph break would have been good).
  2. Interpretation, comparison to other studies.
  3. Interpretation
  4. Explain unusual results, limitations to this approach.
  5. Limitations.  A disappointing way to end!

 

Alex

  1. Summary of results
  2. Justification for this approach (should this have been in the Intro?)

Subheading (the only one)

3. Summary of other studies

4. Introducing their conceptual model

5. Similar models

6. Their model

7. Explication of the model

8. Vertical gradient

9. Age gradient

10. Relation of the two

11. Intro to applications

12. Relates to results

13. Other studies

14. Value of this model

 

Dan

  1. Summarize results, compare to earlier results
  2. Interpretation, "First"
  3. "Second"
  4. "Third"

Subheading

5. Interpretation, other studies

6. Interpretation, our study

7. Interpretation

8. Interpretation

Subheading

9, 10. Interpretation

Subheading

11.  Sounds like results explaining other results.

12.  Other studies, interpretation

13. Interpretation

14. Summary and Conclusion.  Last sentence includes futures questions, implications.

 

Maddy

  1. Summary of results, comparison to other studies (no references), interpretation.
  2. Subheading: result, other studies, interpretation, future need.
  3. Subheading:  result, other studies, interpretation
  4. Other studies, four possible explanations, interpretation of results.
  5. Future research
  6. Subheading: previous studies, interpretation, limitation, implications
  7. Implications for C balance.  Relates to problem statement in the Intro.

 

Yige

  1. Methods (how to classify)
  2. Interpretation
  3. Background
  4. Comparison to other studies
  5. Interpretation (surprising result)
  6. Explanation, continued.
  7. Comparison to other studies.
  8. New subheading:  Interpretation, comparison to other studies
  9. Interpretation, comparison to other studies
  10. Interpretation, comparison to other studies
  11. Background on ET
  12. Interpretation
  13. Subheading: interpretation
  14. Interpretation
  15. Subheading.  Results, limitations
  16. Interpretation
  17. More research is needed.  Limitations
  18. Additional factors, future directions
  19. Limitations.
  20. Heading: Limitations and further work
  21. Limitations
  22. Future work
  23. CONCLUSIONS:  summary and limitations
  24. .
  25. .
  26. Policy implications

 

Ge

  1. Summary of results
  2. Recommendations
  3. Results, comparison to other studies, interpretation
  4. Results, interpretation, limitation, future research needs
  5. Limitations
  6. Implications (subheading) required!
  7. Conclusions

 

Zainab, combined Results and Discusison

  1. Background
  2.  

March 6:  Introductions (yours)

Maddy has questions about the organization of topics.  Does the hourglass help?  Most general to most specific?  Or best known to least known? 

Yang has questions about the order of sentences wiithin paragraphs

Ge moved the introduction to the site from the Methods to the Introduction.  Who else needs to introduce their sites?

Alex:  I think I have sentences that don't need to be here.

Dan:  How to choose what papers to cite.  Are these too old?

Zainab:  How my study will address a knowledge gap.

Autumn:  Do I have too much coverage of some topics relative to others?  Is it clear how my study differs from others?

March 8: Discussion (yours)

Ge: It's way too long, six pages.  What can I cut out?

Yang:  After I finish revising my Intro and Results, I'll write the Discussion.

Maddy: More results coming, but I discussed what I have.

Alex:  I wonder if I need more description of the results in the Discussion.  I tried to interpret them without repeating them too much.

Zanab: I'm improving my statistical analysis, and that will affect my results.  My word limit is 4000 words.

Dan:  I wrote about the results I have, but I will have more.  I highlighted where I summarize results in the Discussion.  Also, I organized within subsections.

Autumn is backing off the grandiose objective of saving the world from fossil fuels.  Like Dan, organized within subsections.  I went back to the Outline exercise.

I have a lot of comparisons of my results, which is hard to do without repeating the results. 

March 20:  Feedback for Improvement

https://docs.google.com/document/d/1fnvBsewyNm_uikI2FCqWjgEL_Rx6rP72CBgJCzwuDrU/edit

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

Jan 18: Intro Presentations (and Why Publish?)

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

Jan 19: Discuss Getting Started

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

Jan 23: Choosing your Journal

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

Jan 25, 30:  Figures and Tables

5,5,5,5, 5, 3,5

Feb 1: Outline and Objectives

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

Feb 6: Results (yours)

5,4,4,4, 5,5

Feb 8: Materials and Methods (yours)

5,4,4,4, 5,5

Feb 13: Authorship

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

Feb 15: Preparation for peer review

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

Feb 20: Introductions (examples)

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

 

"Specific suggestions for improvement": This was one of those classes that just seemed like overkill. We read through so many intros, and the first 2-3 were fine, but after that, it just became too many. I lost focus and started not to care about what we discuss. Perhaps it would be good to limit the number of paragraphs allowed for the assignment for each submission, or have pre-selected papers supplied by the teacher with examples of different good and bad things that have been included in the papers. Then, have students look at the intros they brought and use the teacher's pre-analyzed intros to try and figure out what the intros they brought are about. This reduces the drone of having to look over paper after paper when instead, we can look at one or two and really get a feel for what it is we are looking for and trying to analyze.

Feb 22: Writing exercise, in class

4,4,3,1, 3,4

"Specific suggestions for improvement": This was my absolute least favorite session. We have many international students and even non-international students who struggle with writing, and even admitted so in the beginning, yet I felt this session was more belittling than instructive. If we are going to discuss the different components of sentences and sentence structure and half of your students say they struggle with this, supplementary materials to look over in class (instead of entire book suggestions) prior to analyzing 'good' and 'bad' writing pieces would be a great help! Definitions of things like subjects, verbs, and other things prior to looking through these writing samples would make a lot more sense than just making students feel incompetent when they can't figure out the subject of a sentence and giving them the "I don't really know how to describe it" answer when they ask how to determine sentence structure. If english teachers can do it, then there is material out there to do it. It isn't insulting to go down to 'basic' levels when it comes to this stuff: it's helpful. Even giving the definitions and basic sentences to look over for practice before tackling the tougher sentences would make the injury of getting the complex sentences wrong a bit less, and it wouldn't add insult to injury either. It would be a better way to teach about sentence structure.

 

In short: I do like reviewing the different pieces to see the pros and cons of each and to look at the sentence structure, but I think more information about sentence structure beforehand is very helpful. Not every person, whether English is their first language or not, is going to be at the same level of writing that others are.

 

Feb 27: Advice, Responses to Reviews

5,4,4,4, 4,5

Mar 1: Discussions (examples)

4,4,4,3, 3,4

 

"Specific suggestions for improvement": Please see above for the Introduction assignment, but replace the occurrence of 'intro' and 'introduction' with 'discussion'.

 

Mar 6: Introductions (yours)

5,4,4,4, 4,5

Mar 8: Discussions (yours)

5,4,4,4, 4,5

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

 

Reviewing couple of papers relevant to our own field. Writing critical review to a paper relevant to our field and finding knowledge gap. More practice on grammar and sentence structure improving poor manuscripts(examples).

 

Mar 20: Mid-semester feedback

5,5,4,3,4

Mar 22: Readings on Peer Review

4,4,5,3,5

Mar 27: Ethics

4,4,5,4,5

Mar 29: Statistical Considerations

5,4,5,6000000,5

Apr 3: Proposals

5,4,4,4,not sure

Apr 5: Readings on Publication Productivity

4,4,4,2,5

Apr 10: Reviewer feedback and help session

5,4,5,4,5

Apr 12: Writing exercise, in class

5,5,3,3,4

Apr 17: Abstracts (examples)  Homework:  Make copies after annotating it to show your analysis.

4,4,4,4,4

Apr 19: Work session

5,4,4,? Not sure what this sessions means/entails,4

Apr 24: Abstract, title, keywords (yours)

5,4,5,5,5

Apr 26: Steps to Publication

5,4,5,5,5

May 1: Last Class (Final Steps)

5,4,4,4,5

Specific areas for comments: 

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

Pairs or triples, trading feedback in class

Trading feedback in class has always been a healthy communication. However, it would be great if the communication is between the like pairs or those who have similar background in the relevant field. Otherwise, triples is preferable.

I think this depends on the quality or quantity of review comments that one wants to receive. If it takes a long time to read, I think it is better in pairs. If the document is 1 page in length, the more eyes the better.

I like triples more than pairs for trading feedback

I prefer pairs. It's more focused and effort is not divided between three papers.

^I agree with this. I like pairs. It also takes the pressure off slow readers like me so I can fully take in what the section/paper is saying.

Pairs are fun to do, this can help finding mistakes one reviewer might missed. Two sets of eyes are always better than one.

 Peer review (one so far, one to go)

 This is my first experience as a peer reviewer. There is still a lot to learn as we review other manuscripts that actually helps us to improve our own work.

This is the most valuable thing I have gotten out of this class. I felt more confident in my editing abilities to review another students' work, and also I received excellent feedback from my two reviewers.

I like peer review. Though most students in the class are not familiar with my area, I received lots of great comments

Peer review is a great exercise. It is a great way to see an example of another's work and compare it to your own. If there is something they're doing is or isn't working and that information can be used to better your writing.

I like the peer review because people catch things you might miss because you know the 'know how' of your field.

Peer review is especially important because this helps to learn the actual process of publication.

Informal peer assistance outside of class

Not sure how essential this is, depends on the opinions from everyone's advisor.

 

Not applicable, I have not had peer assistance outside of class.

 

No idea for informal peer assistance. They might point out some mistakes that we are unaware of, so it might turn out valuable.

 

Always helpful to have another pair of eyes look over something.

 

If I have the time, sure! If not, then maybe make it optional??

 

I did not try this with classmates, but look forward to doing so if others are interested.

 

Group discussion

I find this to be the most useful part of class. It is great to hear where people are coming from, and also to hear other opinions!

 

I find group discussions supportive and helpful.

 

This group is very open to comments. It makes it easy to speak up.

 

I like the diversity of the group and that we take notes of what everyone says to look back on. Keep that up please!

 

Going around the table to equalize participation

Giving everyone same ability to participate around the table gives me equal volume from either end.

 

Wonderful.

 

It's nice to hear where everyone is at and to know everyone has concerns. We're all in this together.

 

I like that I have to at least say something during this time. It helps me stay engaged and encourages me to try and keep on top of the work.

 

Class notes

They are a good source of reinforcement.

Having the notes to go back and look at is a nice reminder of what was discussed in class.

I like the class notes a lot. Also appreciate the schedule in the beginning.

As these are the main reference for what has happened in past classes, they are extremely useful. Although, I feel that looking at class notes takes me exceedingly longer due to poor orgnization.

 

 

Potlucks!

It's a good friendly gesture.

Sure.

If I got food to bring and time to spare then sure!!

 

 

PARTY!

 

A must! Why not? Maybe once every time a paper is published from this class.

 

 

Electronic midterm evaluation

I believe it's encouraging in terms of identifying areas for continuous improvement and gives an opportunity to discuss concerns about areas of difficulty related to the student mentoring and self reflection.

 

It keeps things anonymous and that encourages true thoughts on an assignment. <this!!!

 

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

 

I think diversity is fine. People can pick up the simple mistakes or inconvenient ways of communications (sentences) that are usually ignored by the experts.

 

It's good to have knowledge from a diverse group of papers as it allows me to learn something new that I might not see anywhere out of this class. It may ignite interest in other's field.

 

I like reading the different types of papers, but I don't feel as confident commenting on the science of those I'm less familiar with. I feel like having informal outside reviewers can compensate for that.

 

I think it's important to have this diversity available and not restrict the students coming into the course because their paper isn't within 'assigned topics'. There's no other course like this at ESF and having the opportunity to take this time and time again to learn how to become a great author is invaluable. If we restrict what papers we read because "we aren't in that field", those authors will lose out on learning how to publish and WE will lose out on learning something outside of our thesis or dissertation bubble.

 

Diversity is desirable if the meaning of the paper is generally understood. I appreciate the diverse topics, but it might be helpful if the writers can prepare some extra information (ex. Q&As) for their potential readers to understand some difficult terms.

5.  Other comments or suggestions

Sometimes it is hard to express your thoughts and experiments in academic words. There should be some appropriate mentoring ways to help students who are in a half- baked situation to improve their comprehension and expression style.

 

Spanning out when assignments are due. Seemed like a lot is due back to back when things could be stretched out more, like a section a week instead of two.

 

From this class, I not only learnt the processes involved to publish, but also feels way better when in such a "paper publishing support group". Although it is still the middle of the term, but I felt this class goes beyond to just a publishing class, but also gives a sense of community and support instead of working alone or just with your co-author(s). 

Updates

Ge:  I revised the Methods and Results, and I'm going to work on the Intro and Disc.

Yang:  I'll finish it tonight.

Maddy:  I got my results later than I expected.  It's coming along.  It's smoother the second time around.  I'm planning to get it done by Wednesday.

Dan:  Methods, new graphs, I'm working on the Discussion.  Hopefully I'll get to the Introduction before Wednesday.

Zainab:  I'm done with Introduction and Methods, working on Results and Discussion.

Alex:  I have revised Methods and Results, new table and figure.  Intro done, Discussion in progress, sending it to my coauthor before the next round of review.

Autumn: I will have a rough draft.  I am completely switching around my paper.

 

How to handle revisions

www.dartmouth.edu/~mpayres/teaching/gradprogram/HowToRevise_MPA.pdf

 

Assign reviewers

 

Expert reviewers:

https://docs.google.com/document/d/1iztkbyF8zRQbT-mFEWdcNPJLeE5F8kk-HZRA-kazWN4/edit

 

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)."

 

March 22:  Peer Review (Readings)

Review assignments:  Dan → Zainab → Autumn → Alex → Ge → Maddy → Yang → Dan

 

Done: Yang, Ge

Maddy has new results but there is still more to do.  Aiming for Sunday night.

Alex: waiting on a co-author.  Aiming for Friday.

Dan: Discussion and Introduction.  Aiming for Sunday.

Zainab has a draft.  She is hoping for input from a co-author.

Autumn is aiming for Friday night.

Ruth is heading out of town Monday night.  Copies that she has by class on Monday will get done on time.

 

Drawbacks of Peer Review

They sent out one paper to 45 experts, reviews ranged from 1-5 in 8 categories.  Not reproducible! 

 

How to write an influential review

It's important to accentuate the positive. 

It's worse to suppress an important contribution than to publish a questionable one.  Wrong ideas will get corrected later.

 

A troubled tradition

Time to rebuild trust among authors, reviewers and editors.

A survey of medical researchers, 60% said that reviewers did not read their work carefully.  Conflict of interest could cause reviewers to delay.

 

Cistron and Imunex

Cistron submitted a paper, which was reviewed by a rival at Immunex, who rejected the paper and patented the gene sequence (with an error).  Nature published the Imunex version and didn't reveal that they had an inside tip from Immunex that caused them to not publish Cistron's paper.

 

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.

 

Nepotism and sexism in peer review

Women had to have better credentials to get fellowships than men did, based on >1000 applications.

 

Gender bias in the refereeing process?

Editors of 24 primary research journals in ecology and evolution 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 (based on names, assuming only two genders).  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).

 

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.

 

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?

March 27: Ethics

 http://retractionwatch.com/

Outlier: 139

If you see results that don't look right, do it again.  If you get the same result, you believe it.

A statistical outlier can be defined (e.g. 1.5 times the interquartile range, 3 times the standard deviation)

In this case, they might be able to explain the outliers.

The model fit is not very convincing and we don't know what range would be an acceptable

If you have to question something because it gives you a grimy feeling inside, you probably shouldn't do it.

Conflicts of interest: 142 industrial, 144  competition

A student's work is funded by a company that will need to approve her work.  The professor was not forthcoming about the sources of the funding or the conditions of the work.

Who can you talk to if you have a problem with your major professor?

Friends who have nothing to do with your work may be more objective than you are.

Another professor whom you are close to. 

Official channels:  Dean of Graduate Studies, Scott Shannon.  Chair of the department.  Your committee.  Grad Coordinator.

What about talking to the professor?

 

Ed's work would be advanced if he could use materials developed by a collaborating lab, but the other lab is not cooperating.  A post-doc believes that they just don't want to share.

Ed could offer authorship if warranted.

Ed should start in his own lab, starting at the bottom of the hierarchy.  The two directors should work it out. 

Allocation of credit: 145 

Ben talked to a researcher at a conference who used his ideas without giving him credit.

Ben should talk to his advisor.  Is failing to credit Ben worthy of

Authorship (credit): (146,) 147,

Hewish got a Nobel Prize for the discovery of pulsars and Bell, the grad student who first noticed the anomaly, was overlooked.

 

Two grad students and an assistant professor are in conflict over how many papers to prepare.  The professor benefits more from one important paper.  The grad students benefit more from each leading one paper as long as they are each publishable.

The professor could research the criteria and standards for promotion and tenure to see if it's true that it matters.

It's the responsibility of the person with more power to identify the conflicts of interest.

Misconduct:  148, 149, 150

A student makes up a title and author list for a paper and claims that it's submitted when it's not.  The student is dismissed from the PhD program and denied a masters degree even though he met the requirements except for this ethical breach.

 

Francine realizes that Sylvia is fabricating data.  She and their professor both rely on her data.

"I'd like to see what you're doing, because it's important that I understand your results.  Yours look better than mine"

 

April 3: Proposals

Updates:  Dan, Autumn still working on it.  Maddy just finished.  Zainab has a new edition.  Pu Ge was the first to get all his reviews back!

What's in a proposal

Cover Page, Cover Letter

 

Abstract

'Project Summary'

Written in future tense instead of past tense.

 

Introduction

Motivation for the study.  Why should we care?

Different agencies require different sections.  'Introduction and Rationale,' 'Situation and Need,' 'Long-Term Goals.'

 

Objectives

These may come at the end of an introductory section but may be before background.  Get them in early!

This may be a place to match tasks to your research questions.

There may be headings with narrative under them.

They may be numbered or bulleted (rarely just a paragraph as in a manuscript)

 

Background

Context, previous research

'Rationale and Significance'

 

Methods

'Research Approach,' 'Experimental Plan,' Technical Plan,''Experimental Approach.'

Site Description, Study Area (or this could be in the Introduction)

Field Methods, Experimental Methods, Experimental Design

If possible, link your activities to your Objectives or Hypotheses

You may be required to include Education or Outreach, depending on the competition you are applying for (USDA-CSREES had these categories).

Stakeholder involvement

Statistical Analysis

Pitfalls and Limitations (don't do this unless it's required)

 

Figures and Tables

Before modern word-processors, figures and tables were at the end of the text.  Now, most of them are embedded in the text.

 

Expected Products and Outcomes

'Project Deliverables'

 

Relevance to the Organization's Mission

 

Timeline

Bulleted schedule, arrows, table with X to mark activities, tables, outlines'

 

Collaborative Arrangements

 

Response to Previous Reviews

'History of this Proposal.'  This may or may not be required, but it's a good idea to prevent one review panel from telling you to do the opposite of what the last one said.

 

References

'Literature Cited'

 

Budget

There may be a required format or an electronic form.  It looks like a spreadsheet.

There may be a separate Budget Justification.

 

Investigator Qualifications

CVs: These may be limited to 1 or 2 pages, or there may be

Results of Prior Support (required by NSF), Progress Report

Statement of Success with Similar Projects

Investigator Qualifications, with publications

 

Conflicts of Interest

People on this list are not allowed to review your proposal.  People from the same institution, co-authors, collaborators (last 4 years or 5 years depending on the agency), those with consulting affiliations, advisor, advisees. 

 

Current and Pending Support

 

Assurance Statements

 

Other differences from papers

Deadlines

Page Limits

Read the Directions!

Talk to a Program Manager.

April 5: Publication Productivity (readings)

 

Resumes were assigned male or female namesChanging patterns of publication productivity: accumulative advantage or institutional isomorphism?

Rates of publication of papers and books depend on the type of institution: Faculty at research university, doctoral universities, comprehensive (professional, masters, and undergraduate), liberal arts 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.  (like the tail of a snake?)

 

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).

 

Publish or perish?  Some reasons for perishing.

They think it's not worthy (they didn't do an adequate literature review).  They are too busy.  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.  If you don't publish, what was the point of doing the work.

 

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.  Co-authorship should be valued.  Quantity vs. quality.

 

Cumulative disadvantages in the careers of women ecologists (1993)

Survey. 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. 

Women are less satisfied with their PhD advisor.  They have a harder time finding a mentor.  Lower salaries, career advancement, productivity.

 

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

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

High ego strength.  Personal dominance.  Preference for precision and exactness.  Strong impulse control.  Preoccupation with ideas and things rather than people.  Autonomy, self-sufficiency.  Chemists, physicists, biologists. 

 

Apr 10:  Reviewer Help Session

Progress reports

Dan is getting help from Adam on stats and graphs.  They will talk this week.

Autumn's thesis is due Saturday.  She will finish getting results today.  Now she is applying four different models. She will bring some part of the manuscript version.  Maybe stats and graphs.

Maddy is reading literature to improve her Discussion.  Still working on stats and graphs.

Yang is working on revisions this week, then it will go out to the co-authors.  Maybe Discussion.

Pu Ge is going through the review comments and waiting for comments from his co-author, hopefully on Wednesday.  The Getting Started Exercise could help align the Intro and Discussion.

Alex is reviewing the comments from the last review and working on presentation of statistics.

Apr 12: Abstracts (examples)

Analysis of Abstracts

What's in an abstract?  Pick one, analyze it.  Color code it, then upload it to the google folder for background presentations.

Problem statement:  Yellow

(Background): Brown

Objectives: Red

Methods if novel:  Light blue

Results:  Dark Blue

Interpretation, Applications, Conclusions (Discussion):  Orange

 

 

Pu Ge

  1. Background
  2. Background (opportunity)
  3. Objectives
  4. Methods
  5. Methods
  6. Discussion (no results!)
  7. Conclusion, good match for the (implicit) problem statement.  This is where we learn that the attempt was a success.

 

Yang

  1. Background
  2. Problem
  3. Objectives (and Methods)

4-9.  Results

10.  Conclusion (better than the question, go back and change the question)

11.  Future research needs

 

Dan

  1. Problem
  2. Objectives, with location
  3. Methods (maybe not needed)
  4. Result
  5. Discussion
  6. Result
  7. Discussion
  8. Discussion (of Results not presented) 

Poor match between the conclusion and the problem statement.

 

Autumn

1-3 Methods

4 Result

5 Method

6 Result (and Discussion)

7 Result and Discussion

8 Result

We discussed whether the first sentence involves objectives.  But there is no background and no problem statement.  And no conclusion.

 

Maddy

  1. Background
  2. Objectives with study location
  3. Methods

4-6. Result

7.  Discussion

8.  Result

9.  Interpretation.

10  Result and interpretation

11.  Conclusion, missed opportunity for a better problem statement

 

Zainab

  1. Good problem statement
  2. Objectives
  3. Background
  4. Methods
  5. Results
  6. Interpretation
  7. Intrepretation

Conclusion should have been that Milo seed oil is promising!

 

Alex

  1. Problem statement
  2. Objectives
  3. Methods, location

4-7 Results

8  Method, Result

9  'We propose that'' tells us that they are speculating

10

Send them the

 

           

 

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

https://dl.sciencesocieties.org/publications/style

Literature citation

Apr 17:  Help with Revisions

Status: How's it going?

Alex:  Working on presentation of statistics.  And formatting the bibliography.  He brought the statistical methods section.  How best to present the design.

Zainab:  Working on statistics and evaluation of my results.  In the process of writing my conclusions, distinguishing my work from that of others.  Results and Discussion.

Pu Ge:  80% done addressing the comments.  The biggest problem is the Getting Started Exercise.  Some of my objectives are addressed in the Discussion but not the Results.

Maddy:  I redid my results and I have trouble verbalizing them.  What's the best way to get help with that?  I made a chart of the significiant results.

Yang:  I don't have anything for today.  I reviewed the comments and I think I have a better way to organize the introduction and discussion.  Problem statement:  Hg contents of trees.  What about wood burning?  That contributes only 1% of Hg pollution.

Dan:  I have some graphs, I want to ask Yang for help with statistics.

People who want another review:

Maddy, next Tuesday

Pu Ge, this Friday

Zainab is waiting for review comments from Dan

Alex is willing to review but doesn't need another internal review.

April 19: Statistical Considerations

Yang:  GLM

Maddy:  GLM, ANOVA

Pu Ge:  map accuracy statistics

Alex will be at the same meeting as me (ANOVA)

Dan:  GLM with ANCOVA, simple regression, on count data

Zainab:  three-way ANOVA

Autumn is fitting a model, sorry I don't know more, she's out sick

 

April 24: Abstracts

Maddy: I did a lot of editing and I went to the Writing Center and they helped with the flow.  There is a sentence I highlighted that may not belong--I'm over the word limit if I leave it in.

Yang:  I don't have a good problem statement. 

Alex:  I don't know how to analyze my data.  I need to block by tree.  It's hard because the sampling design is not balanced.  My P values will change.

Pu Ge:  My main concern is the length.  It's 400 words.  My journal doesn't have a word limit, but I think it's too long.

Autumn:  I wrote 338 words and brought it down to 231 (250 is the limit).  For my thesis, it had to be 150, but that one is not as good. 

Dan will finish his paper tonight.  The abstract is short.  The results are likely to change.  Word limit is 250, does he need to add anything?

Zainab:  I have reduce my abstract from 360 to 256, but it needs to be 250 at most.  I'm working on my problem statement.

 

April 26:  Steps to Publication

Electronic submission of manuscripts

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

https://drive.google.com/drive/folders/0BxXuVrpNGuD9U1pwQVZhdnJRamM

 

May 4: Final Drafts 

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