January 13:  Why publish?

Papers we're writing this semester

Ali Pracha:  FNRM,  Energy return on investment for four major food crops in Pakistan.  Finishing a MS.

Matt Dey: GPES, MS, final semester.  Organic food and theory of planned behavior.  People's perceptions of mortality.  Undergraduate in business.

Michaela Labrioli. GPES, MS, final semester.  Foresters attitudes towards climate change and impacts on NYState forests.

Carlos Alvarez, Mexico.  Second semester PhD, EFB.  Rare and endangered plant species.  Cycad species, coexistence, ecophysiology.  Population structure.

Andrew Mishler, FNRM, MS final semester.  Discolored wood in sugar maple, attributed to landscape and tree characteristics.

Rachel Ribaudo,  FNRM, MS final semester.  Rate and source of discharge into Nine-Mile Creek, temperature and chemistry.  Pollution from Allied Chemical gives a chemical signature.

Lisa Kurian, FNRM, hydrology.  Winter nitrate in the Adirondacks as affected by snowmelt. 

Kathleen Baier, EFB, MS final year, molecular biology of American and Chinese chestnut trees.

Chengjun, EFB, MS final semester.  Best field stock to grow bacteria to produce biodegradable plastics.  How to treat wood chips, or how about glycerol, a by-product of bio-diesel production.

Qin, Chemistry, 3^rd year of PhD.  Biodegradation of plastic.  Quantitative RT-PCR, which genes are active. 

Why Publish?

Kathleen:  Make the information available for researcher who need to know what's already been.  Participate in the incremental growth of knowledge.

Michaela:  Obligation to the people she surveyed.  They are expecting her to share their opinions.

Ali:  We will learn how to critique a scientific paper, by doing peer reviewer.  We will become more critical readers.

Juan Carlos:  Personal recognition.  Earn more money.  Career advancement.

Rachel:  Publishing is important for getting to your conclusions. 

Chenguin:  There are a lot of bad papers out there.  We want to provide only what we really learned.  We can correct wrong ideas, too.

Andrew:  Exposing people to what you did.  If you don't publish it, nobody will know about it. 

Chin:  Summarize my work, and plan future work. 

Matt:  Publication provides a motivation to do our best work.  It's more than just a thesis.

Lisa:  Makes you more competitive in the job market.

What's hard about it?

Andrew:  How to select what's important to report.

Michaela:  How to present a descriptive study.

Juan Carlos:  How to write concisely.

Rachel:  Connecting all the points, all the results together.

Michaela:  Appropriate writing style.

January 20 - Knowing Your Journal

1. Factors that are influential in your selection of the most appropriate journal for this particular manuscript. 
   1. Appropriate audience for the discipline, which in Matt's case is interdisciplinary.
      • Who subscribes?  Michaela has a website with this information
      • Where are the papers published that you perceive as being similar to the one you're going to write?
      • The journal will declare what types of papers it's looking for.
   2. What points of view are represented?  Some journals are more traditional and some invite "commentary."
   3. Reputation.
      • Science Citation Impact Factor:   see reading on my web site
      • Who's on the Editorial Board, their reputations.
      • Opinions of people in the field
      • Which journals are being cited in the papers your read
      • Older journals have more time to establish a reputation
   4. Length of time to publication
      • The journal web site may provide an indication of the timeline they aim for or data on their performance.
      • The papers have dates on them.  They may have a fast turnaround for review but a backlog for publishing!
   5. Chance of acceptance.
      • Some journals publish their acceptance rate
      • Matt found a document on line that listed acceptance rates
      • Opinions of experienced people in your field
      • You can ask the journal.  We agreed to find out about the following journals: Ali: Energy; Matt: British J. of Social Psychology; Michaela: J of Forestry; Andrew: N. J. Appl Forestry; Chengjun:  Biotechnology Progress; Rachel:  Hydrological Processes; Katheryn:  Molecular Plant Pathology; Qin: Applied and Environmental Microbiology
   6. Do they encourage student papers? Molecular Plant Pathology asks students to identify themselves and offers a prize.
      • They advertised this on their web site.
   7. Cost
      • Instructions to author
   8. Length
      • Some journals don't want long papers.
   9. Availability:
      • Society journals are available to members, if they subscribe
      • What libraries subscribe?  See the web site Michaela found
      • How much does a user pay to get your paper?

2. You selected the following journals

Qin: Applied and Environmental Microbiology, because most of the papers she uses are published there.  Her advisor recommended it.  If rejected, Applied Microbiology and Biotechnology.

Katherine: Molecular Plant Pathology - but we don't get it.  History of the project.

Rachel:  Hydrological Processes - recommended, impact, use it a lot

Chengun:  Biotechnology Progress - recommended by advisor, his lab

Andrew: J of Forestry  - audience.

Michaela: J of Forestry - survey population subscribes to it.

Matt: British J. of Social Psychology vs. J of Environmental Psychology

Ali: Energy - reads their articles, impact factor looks good, mission statement was relevant.

4. Does your journal specify
   • length of the text

typewritten double-spaced: figure 200 words/ page, 4 pages of your text to 1 page in journal format

British J of Soc. Psych. : 7000

Journal of Forestry: 4500

Biotechnology Progress: 8 pages or fewer, double spaced.

Hydrological Processes: 7500

Molecular Plant Pathology: 7000, also 150 MB total

Applied and Environmental Microbiology: charges more for papers longer than 8 pages.

Energy: appropriate

• • length of the abstract

British J of Soc. Psych.: 100-200

Journal of Forestry: 130

Forest Products Journal: 250

Biotechnology Progress: <250

Molecular Plant Pathology: 250

Applied and Environmental Microbiology: 250

Energy: not more than 200

• • number of figures or tables

Molecular Plant Pathology: 150 MB for the whole file

• • page charges

Qin: $75/page, $250 over 8 pages.

Ali: $485/page for color illustrations

1. • required sections (must results be separated from discussion?  Is there a separate conclusions or summary section?

Katherine:  Summary, Introduction, Results and Discussion, Procedures, Acknowledgements, References, Tables, Figure captions, Figures.

Chengjun: Cover Letter addressing the significance of your paper and keywords,

Ali: Glossary of Technical Terms

January 22, 27 - Figures and Tables

Axis labels define your variable.  Do you need one for "site"?

Units go in parentheses at the end of the axis label.

How do you decide whether to identify symbols or lables in a legend or in the caption?  In Andrew's case, his sites are too many to list in the legend.  Finding the room to fit the legend: they don't have to be inside the figure.  Reading the figure caption is more work than reading a legend.

Fill patterns:  Avoid gray.  Use black, white, and b&w fill patterns.  Black makes it hard to see the error bar. 

Avoid using two y-axis scales for different variables on the same graph: Readers see relationships that aren't real but depend on the relative scales.

Readers expect numeric axes to be linear.  Make them linear if you can.

Avoid scientific notation (1.20E+06).  Change the units to get the order of magnitude right.

3-D graphs:  Don't use these unless you have 3 dimensions (avoid the "unlabled z axis"). 

Avoid shadows and other fancy enhancements that distract us from your message.

Choosing an order for variables

Use uniform fill patterns or symbols across graphs to mean the same thing.

Excel has limitations for graphing, specialized graphing programs can do more.

Don't use these defaults in Excel:  gridlines, fill patterns, box around the figure, box around the legend, alphabetical ordering of variables.

Multiple figures:  If you want readers to compare across figures, use a uniform axis scale.

You can group figures into panels sharing common axes (x, y, or both).

Figure captions can be brief or they can convey part of your story.

Align numbers on the decimal.

Tables:  Values to be compared should be in columns.

Unfortunately, tables can be longer than wide, so sometimes, you can't follow that rule.

When should you use a figure?

It's easier to see pattern in a figure.

When should you use a table?

Some information is not readily presented visually.  Some is too lengthy to be presented in a figure.

When should you use text?

When there is not very much information. Even if you don't have a lot of information, you might choose a table or text to draw more attention to it, if it's important.

January 29

Outlines: helps raise questions that we'll address later:  Authorship, Corresponding Author

Katherine:  What data to include?

Andrew: How much detail in a methods section?  What order to present the results in?

Pat:  How could it help me to use an outline?

Michaela:  What's missing?  Is there too much?  The article has to be short.

Matt:  Order of ideas in the Introduction, which could influence the order in the Results.

Lisa:  Two papers, one on physical and one on chemical results.

Rachel: Difficult to explain the methods.

Chengjun:  How much detail to include in the methods.  Manufacturer and city for an instrument. 

Qin:  The discussion and introduction are the hardest.

Ali:  don't know.

February 3 Results

What level of "interpretation" should be reserved for the Discussion?  There are lots of ways to slice it, depending on the rest of your paper.  I think the meaning of your results should be clear in the Results section.  Err on the side of giving us interpretation, for now, because you're writing this section first.

Katherine:  Will this make sense to an uninitiated reader?  When do I need figures or tables to back up these claims?  "(unpublished data)"  You can say, "(data not shown)."

Ali:  There is not much to say; the results are very short.  Will readers want to see the information? 

Andrew:  Presenting summary statistics without getting to wordy or detailed.  Is ranges a good way to describe soil characteristics? 

Pat:  How to describe the data; do I need to be referring to a figure or a table.

Matt:  What to include given the word limit.  Paragraph construction.

Michaela:  Will the reader understand what I'm trying to say?  If a reader hasn't studied the Methods section.

Lisa:  Tried to move some of what she had in the Discussion into the Results.

Rachel:  How much detail to include:  There could be 2 pages on the data, or it could be not included at all.

Qin:  How much background to include in the Results.  Should some of this material be in the Introduction.

Chengjun:  Cite figures and tables in the text. 

Expert Reviewers: 

February 5 Methods

Ali:

Pat:  What to include?  What's too insignificant to include?

Qin:  Do all the primers belong in a table?

Chengjun:  How much detail on the steps of the procedure?

Lisa:  How much detail to include?

Rachel:  Site description: does some of this go in the introduction?

Michaela:  How much of the survey to include?

Matt:  Same question.

You can't include all your questions.  Think about what the reader needs to know to understand your results.

Andrew:  Site description.  Data analysis.

Kathleen:  Kits, and adjustments that she made to them. 

How to attribute the source of the RNA.

February 10 Literature Review

Two people will try to remember to bring us a laptop with an Ethernet port.  Was it Chengjun and Ali?

How to find?

How to organize?

How to attribute sources?

(We had a RefWorks session, led by Linda Galloway.)

February 12 Instructions to Reviewers

Is the contribution important?

Is it original?  Does it overlap with already published work?

Is it relevant to a broad audience?

Does the paper tell a cohesive story?  Do the parts fit together and flow?

Are the parts logically organized to lead to the conclusion?

Are the paragraphs well organized?  Is the writing clear?

Is language appropriate to the intended audience? 

Proper use of technical terms, e.g. Latin names, scientific units, chemical nomenclature.

Is the length appropriate for the content?  Are there any portions that should be expanded, condensed, combined, or deleted?

Is the description of the methods sufficient to allow a reasonably competent reader to repeat the experiment?

Are the statistical methods appropriate and correctly applied? 

Are there errors of fact, calculation, or interpretation?

Are all the tables and figures necessary?  (Are they referenced?)

Is there duplication of information between tables and figures (or text)?

For the next draft (not yet appropriate for our first drafts):

Is the title appropriate?  Does it clearly and sufficiently reflect the contents?

Is the current state of knowledge adequately reviewed?

Does the introduction lead us to the objectives?

Are the results answering the questions you asked?

Are the conclusions supported by (not exceeding) the results?

Journal reviews will also ask:

Is this contribution suitable to the journal?

Should this paper be accepted, accepted with minor or major revision, or rejected?  Reconsider after major revision?   Reject in current form but consider resubmission?

Publishable but not in the journal?  (if so, suggest a more appropriate journal)  Only if space is available?

What makes a good review?

The reviewer has read the paper thoroughly and understands the topic.

Starting the review with a statement summarizing the paper lets the author know whether the reviewer understood the paper (if not, the paper should be improved).  It also helps establish your credibility.

Be constructive in your criticisms.  Make specific suggestions for improvement. 

Give reasons to back up your observations or suggestions.

Let the author (and the editor) know if you don't have the expertise to evaluate some aspect of the paper.

Reference your comments by line numbers so the author can find what you mean.

Try to identify the most important criticisms.

You can organize your comments into categories. 

If you number your major comments, it can make it easier for the author to respond.

It's nice if you can describe the strengths of the paper and not just the weaknesses.

Humor can lighten a review.  Avoid sarcasm.

Try not to take it personally.

Reviewer assignments

Rachel reviews Lisa reviews Rachel.

Kathleen reviews Chengjun reviews Qin reviews Kathleen

Andrew reviews Michaela reviews Pat reviews Andrew

Ali reviews Matt reviews Ali.

February 17 Introductions

We went though the examples and identified the purpose of the parts of the Introductions, by paragraph.  We started with the shortest.

Kathleen: 

1. Importance of the topic (chestnut and blight)
2. Brings us up to speed on the work of this group.  States the problem area.
3. This paragraph is relevant to objectives but they are not stated very clearly.  It also has methods in it.

Qin:

1. Introduces PHAs, why they are important, background information, and, at the end, the goal (define the metabolic pathways for SCL-MCL PHA production.
2. Brings us up to speed on the work of this group (cites a figure).
3. More background (cites a figure).

3 (cont).  Objectives.  And they tell us what they accomplished.  These specifics could have been written into the objectives.

Pat:

1. Importance, background.  This paragraph specifies radiata pine.
2. Which trees are susceptible.  Extent of pine plantations (not just radiata).  Which pine species are susceptible. 
3. Biology of the insect.
4. Management options.  We still don't know what this paper is about!
5. Objectives.  This is a review paper.

Michaela:

1. Introduces the topic of attitudes towards cities.
2. More specifically, foresters' attitudes towards cities, and the tension between urban interests and forestry.
3. Introduces urban forestry, ends with the problem statement: how do SAF members view urban forestry?
4. Introduces attitudes of urban people.
5. Objectives. 

Andrew:

1. Introduces sugar maple.
2. Importance to lumber production in the region.
3. Importance of wood color.
4. Definition of heartwood, discolored wood.
5. Hypotheses, or things that aren't known: how to predict heart size.
6. How does heart size relate to tree size?
7. Objectives, with a final sentence about the value of the results.

Ali:

1. Background on oil supply.
2. Objective: forecast oil supply.  Disclaimer.
3. Background: geological models.
4. More recent geological models and a review of other methods.
5. Describing results of other people's studies (huge table).
6. Why these methods are not as good.  (setting us up)
7. Economic models, and why these are insufficient.
8. How this analysis should be done (so maybe these are the Objectives).

Maybe the objectives came further towards the front of this Introduction because it was long (2.5 pages).

Chengjun:

1. Background on PHA, importance.  High cost is a problem.
2. Challenges to recovery of PHA from cells (hence the high cost).
3. Review what's been done so far:  Two strategies for separation and purification.
4. Another method (oxidation), advantages and disadvantages.
5. Another method (selective dissolution), advantages and disadvantages.
6. Summarizes the cost problem.  Objectives.  A bit of Results.

February 24 Responses to Reviews

Andrew: We'll understand these better when we have the Introduction. 

Michaela:  Only someone in the field would know what really should have been done and what level of detail is necessary in the methods.

Lisa: This was more complete than the previous things we reviewed together.

Kathleen:  Seeing the Methods and Results together is better than parts separately.

Rachel was involved in Lisa's field work, so it was hard to pretend to be a ignorant reader.

Kathleen: My Methods and Results are in separate documents.

Michaela:  I did that; there shouldn't be a problem pasting them together.

Reschedule writing exercise

Smith's writing is more direct.  The language is simpler.  Paragraphs are good.  Parentheses are not.

How many digits?

1. precision of the measurement
2. what do you need to compare it to?
3. uncertainty in a mean is indicated by the standard error
4. converting units with a constant doesn't add precision
5. You might want to report insignificant digits to make your calculations consistent.

Suggestions for improvement, using anonymous examples.

Methods:  Too much?  Too little?

"Colonies were transferred to ZetaProbe N⁺ membrane (Bio-Rad) and lysed by standard methods (Sambrook and Russell 2001)."

"Stream water and groundwater samples were collected in plastic bottles, which were rinsed twice with stream water or groundwater, respectively, prior to sample collection.  We stored water samples in a cooler on the day of collection and then placed them in a refrigerator at ~4 ⁰C until analysis."

"RNA pellets were dissolved in SSTE following overnight precipitation in 2 M LiCl₂ and the quality was assessed by agarose gel electrophoresis and analysis with the Agilent Technologies Bioanalyzer (State University of New York Microarray Core Facility)."

Use past tense for Results.

Use active verbs.  Use the subject and verb of your sentences to convey the main meaning. 

"A web-based survey of 345 members of the NY SAF was conducted." 

"To ensure confidentiality, the researcher did not have access to the respondent email list and thus a non-response survey was not possible."

"An inspection of the variation across mortality types indicates that there appears to be no significant difference between the mean scores on each scale across the three types of mortality fear."

"Cation extractions were performed"

"Stump discoloration averages were significantly different across sites"

Throw-away phrases or sentences:

In Figure 3

From Figure 4

Table 1 shows that the total inputs are consistently greater than the corresponding wheat yield

Table 1 gives a general description of the eight stands on which measurements were taken.

The results of this analysis are shown in Table 2.

The procedure for measurement was adapted from McNabl (1989, 1993).

Describe your results, citing statistics (don't focus on statistics)

"Best subsets regression indicated that bolts taken at .. were best of estimating whole tree Siricid density"

Ditto for the attitude scales.  Write about the attitudes, not the scales.

"Under each model the significant determinants of the variance in intentions were attitudes and subjective norms whilst each model identified intentions as the significant determinant of the explained variance in behavior."

"The trend lines constructed for nitrogen and phosphorus consumption by Pakistan's wheat crop show steady increases from FY 1998 to FY 2010."

Don't make the reader learn new acronyms. Some journals have a rule that you have to use them more than twice or not at all. Even if you use them more than twice, it might be better to spell out the words if they will be better understood by your readers

"Fossil fuel inputs include high-speed diesel (HSD) oil used by farm vehicles and light diesel oil (LD)) used in irrigation pump sets."

"Diameter at breast height (DBH), species, crown class, and the status of growing stock (AGS/UGS) were recorded for each tree inventoried (Table 3)."

"Landform index (LFI) and terrain shape index (TSI) measurements were used.."

Look at the number of digits you report.  Are they all meaningful?  It doesn't improve the precision of a number to convert the units.  "Their data collection showed that traditional farmers used an average seed application rate of 50 kg/acre (123.55 kg/ha) and progressive farmers 53 kg/acre (130.96 kg/ha). 

Say the same thing if you mean the same thing.  Variety ("elegant variation" according to Fowler) can reduce clarity. "according to the SMART- PCR cDNA Synthesis Kit (Clontech, Mountain View, CA)." "using the NucleoTrap-PCR Purification Kit (Clontech).""as indicated in the PCR-Select- cDNA Subtraction Kit (Clontech). "  "as described for the Creator SMART- cDNA Library Construction Kit (Clontech)." " according to the manufacturer's directions (Clontech)."

Grammar and punctuation rules.  Have you heard of these?

Don't split infinitives

Don't end a sentence with a preposition

Dangling modifiers

"We performed the study on a 4 km reach of Ninemile Creek in Syracuse, NY, a second order stream that flows into Onondaga Lake."

Don't use a comma in a list of two items.

"There is high variation within classified regions, and across regions."

"The cells were harvested at 48 h, and then lyophilized."

"which" introduces a non-restrictive clause; "that" is restrictive.

"IButtons are temperature data loggers that were programmed to record temperature at a  3 hr interval."

Use words for their expected grammatical roles.  Avoid adjectival nouns. 

            "Contained within the attitude set of questions."

Here is a long noun clause being used as an adjective:

"a summated rating scale labeled "attitudes toward climate change in New York scale"

Hyphenate compound adjectives (or avoid using them):

"Three, 10 ul reactions were assembled for each tester and driver sample (Clontech)."

" if certain half meter tree bolts could be used"

"These items reflected consumption related behaviors as well as more knowledge and awareness related behaviors."

"A full-length laccase clone was isolated from the library by colony hybridization with an alkaline phosphatase-labeled, laccase specific probe."

You can't start a sentence with a number or an abbreviation.

1. dentatastem tissue was ground to a fine powder in liquid nitrogen.

86% or 92.1% (v/v) Biodiesel-gylcerol was provided by

Don't use a solidus (/) except to indicate division.

            "primers specific to the C. mollissima laccase/diphnol oxidase fragment."

Include a referent with "this" or "these".

"This was included in order to determine the importance of environmental attitudes"

Avoid the possessive apostrophe, which is rarely seen in technical writing.

            "Contained within the attitude set of questions were items designed to reflect participants' views on the impact of organic food on both the environment and human health."

Don't use pretentious words where a common word has the same meaning.  To me, these sound affected:

"impact" for "effect"

"comprise" for "compose"

Phrases to omit (you can find long lists of unnecessary phrases in books on writing)

"in order"

"Finally, 5 items were included to capture a wide variety of behaviors in order to reflect the variety of possibilities for interaction with the organic food movement."

"Respectively" rarely improves a sentence.

"Due to the genes fadA, fadB and fadAx, fadBx are on the same operons respectively, only genes fadB and fadBx were selected to check by QRT-PCR."

Some problems with presentation would best be avoided when choosing your methods, by thinking about how you are going to explain them in print. 

"The final item related to organic food consumption as a child and was measured on a 5-point scale while all other items in the second section of the survey were measured on a 6-point scale."

Discussions

Reference your results without repeating them.  Reference your tables and figures wherever relevant.

Interpretation, including alternative explanations.

Address problems with your work.  Other studies may help explain problems.

Comparison to other studies.

Limitations to this approach.

Suggestions for future research.

Practical implications. 

How generalizable are these findings?  Population of inference.

Conclusions: relate back to the initial problem statement

Chengjun

1. Comparison of the new method to conventional methods.  (Very impressive.)
2. Disadvantages of the other methods.
3. Conclusions:  summarize strengths of the new method.

Michaela

1. Reminds us of the purpose of the paper
2. Other studies in this area (could have been in the Intro).
3. Summarize results, highlighting the most important points.

4, 5.  Why this is important and what it can be used for.

This Discussion doesn't explain the results but focuses on implications.

Kathleen

1. Previous work from this lab (odd that we didn't get this in the Introduction).
2. Background.
3. Relating results to those of other studies.
4. Background?
5. Interpretation, importance.
6. Interpretation, ending with a suggestion for future study.

Qin

1. Motivation for this research.
2. More on the importance of this research.
3. Other studies.
4. Previous work from this lab, context for the current study.
5. Interpretation of results.
6. Advantages and disadvantages of this approach; future research (under way).
7. Interpretation of results, implications, possible future research.
8. One sentence on conclusions.  Future research.

Matt

Subheading: Prediction of intentions

1. Interpretation and reference to other work.
2. Interpretation, problems (unexpected results).
3. Comparison to previous work.

Subheading: Perceived need

4. Interpretation and reference to other work.

Subheading: Prediction of behaviour

5. Interpretation, limitations of this approach.
6. Explanation, practical implications.
7. Interpretation and reference to other work.  Limitations of this approach.

Subheading

8. Interpretation.  Suggestion for future research.
9. Interpretation, comparison to other studies.  Practical implications.
10. Summary and Conclusions.

Andrew

1. Summary of results
2. Comparison to other work.
3. Implications, other work.

4, 5, 6.  Limitations to this approach. 

7. Sensitivity analysis: how big a problem is it?
8. Another limitation to this approach.
9. Conclusions, importance. 

Rachel

1. Advantages of using this method
2. Advantages of using this method

3, 4.  Results, comparison to previous methods.

5, 6, 7:  Problems: model assumptions, errors, spatial variation.

New heading

Recommendations for how to use this model:  Practical application

Heading: Conclusions

What was accomplished

Errors and limitations

(long and repetitive)

Lisa

1. Question

Snowmelt

2. Interpretation (mostly results)
3. Results, comparison to other studies

next heading, next season

4. Results and interpretation

Question (heading)

5. Results and comparison to other studies.

Question heading

6, 7.  Results and interpretation

Question heading

8, 9, 10.  Results, interpretation, comparison to another study.

Heading

11. Interpretation, other studies

Conclusions

Ali

Results and Discussion.

3.1 First paragraph results, 2^nd paragraph discussion

3.2 Results

3.3  Result, comparison to other studies

3.4  Results.  Comparison to other studies. 

Conclusions

1. Summary, recommendations.
2. Importance.

March 3 First drafts of Introductions

Chenjun:  How much to include?  His is short.

Qin:  Maybe the opposite: is this too long.

Kathleen:  Started out with a lot of elementary background information.  Reference management and citation issues.

Rachel:  How much to explain what's wrong with other methods?

Lisa:  She realized that she was writing some things that belong in the Discussion.

Andrew:  Keeping it relevant to the rest of the paper.

Michaela:  How climate change could impact northeastern forests: this section needs to be cut.  Needs more about why this study is important.

Matt:  I know what I'm trying to say, but am I explaining it well enough to other people.  How to order the three sections. 

Ali:  How to justify the choice of crops.  Background on the crops.

March 5 First drafts of Discussions

Qin:  Worried that she might be missing some points.

Andrew:  Writing the Discussion made me realize that I wanted to add to my Results.

Ali:  The paper is still changing like you wouldn't believe.

Matt:  It's hard not to repeat your results when comparing them to other studies. 

Lisa: Ditto.  How much is enough for referring to your results.

Michaela:  Mine's a disaster.  I have limited space, so I have to decide what's important.  It might not be interpretation, but implications, take-home messages, and what comes next.  Problems with the study, so that future studies benefit.

Kathleen:  This was the most difficult part so far.  Since my Intro didn't have specific hypotheses, I find myself introducing material in the Discussion.

Lisa:  Would it be easier to write the Discussion first?

Rachel:  This is a Methods paper.  The method didn't work out perfectly.  In fact, it disagrees with another method by an order of magnitude.  It's not clear which one is wrong.  Should this paper focus on the methods given these limitations?

Chengjun:  What needs to be addressed?  I went through the Results and discussed each of them.

In comparing results to other studies, I found contradictory results. 

Qin:  One of my conclusions conflicts with another study.

Reminder:  Outside reviewer

March 17  Midterm Feedback for Improvement

Why Publish?  "less useful" "good for introduction to the course"

Discuss Getting Started "most useful" "good for centering on specific goals and paper objectives" "helpful before starting writing"

Steps to PublicationChoose Journal "useful" "somewhat useful" "very useful" "good for journal requirements"

Tables and Figures: 5 usefuls, "limit how many we try to review" "useful for understanding the instructor's preferences."  "very useful" journal requirements, general advice. 

Outline: "always helpful in writing a paper" "introduction to document maps, styles, and headings very helpful." "useful" testimony "help focus" "especially useful"

Results: highly rated

Materials and Methods: highly rated

Writing exercise (replaced with RefWorks):  3 comments that this was too late.  Drop this next year.  The library is offering a graduate level seminar.  We realize four semesters later that we should have gone to a librarian. 

Preparation for peer review: could have been done in less time, useful, useful.

Introductions (examples):  "not very useful, our papers are so different" "most useful" "examples were helpful to writing my own""we should have read them ahead of time" "useful"

Statistical Considerations: 4 not so useful,  not so useful.  How about making it optional, for people who need help.

Writing Advice:  "examples are not anonymous" "useful" "useful"

Introductions, Discussion (shared in class):  highly rated.  Helps identify problems.  Should we exchange them in advance.

Work session: the more the better, MOST HELPFUL, team up by sections,

Readings on Peer Review: 

Authorship: 

Writing exercise:  "how much could we accomplish in one session?" "not a priority""less helpful""we could always improve"

Proposals:  "helpful" "not for me but for the future"

Abstracts: 8 positive

Work session:

Ethics "most helpful" "we have heard about this a million times.  Are there special concerns?"
not a priority" "might be helpful"

Scientific careers and role of publications

Abstract review

Galley proofs

Ways to work together
several "feedback in class" "pairs work better than triples, but it depends on the length" "less helpful, because it's so short"

Group discussion is good (2)

Going around the table

Writing formal reviews outside of class

Content area:

Pair by content area.  Ditto, ditto.

It's helpful to get the point of view of an outsider.  For peer review, it's more important to have someone

Give a presentation at the beginning of the year.

Getting Started Exercise

Other Suggestions:

Things are flowing well, and our papers are coming together.

Direct feedback, but too much feedback can hamper the writing process.

I would suggest this class to others and it should be offered every semester.

Suggestions for  next year:

Everyone should give a presentation on their topics

Table and Figure exercise is not helpful in all cases.  Bring multiple versions of a table or figure if you have a question about which would be best.

Sharing documents in advance

Responses to Reviews:  we shortchanged this year.

Set up Blackboard for posting documents.

Suggestions for us:

More reviews?  Not more formal ones.  More informal ones.

Reviewing the same paper as before.

We revised the syllabus.  I'll distribute that separately.

March 19: Sections for Review

Ali: Methods section needs to be shorter.

Matt:  Redid his methods section.  Part of the introduction: Hypotheses.  Does this format work better than before.  He improved the figure, is it too confusing?

Andrew: Results, make sure that the order is logical.  Is there enough description of the results?  It might be too brief.

Michaela:  Methods, are they clearer?  Check the scales on the new Tables and Figures.

Rachel:  Introduction:  Is it specific enough?

Kathleen:  She is adding material to the paper.  She wants advice on how to fit it together. The She brought the parts that want attention.

Qin:  Discussion:  Not sure about the organization, whether she has missed anything.  She is redoing a set of experiments, under different conditions.

Chengjun:  Introduction.  It was very short, and he got advice on what to add (why this carbon source instead of others).

March 24:  Readings on Publication and Peer Review

Michaela:  Motherhood and scientific productivity

Women researchers in Norway published 3.5 articles/3-year period, while men published 5 articles/3 year.  This has been attributed to child-rearing.  But women with children over 10 are productive.  Unmarried women were less productive!  Women in senior positions were as prolific as men in similar positions, but fewer women are in them.  Marriage had a negative effect on productivity for men.

Rachel: Equity and Equality in measuring Faculty Productivity

Men and women are different and so you have to be careful what you compare.  Women write more books, men write more journal articles.  Women spend more time mentoring students.  Presentations, reports prepared for sponsors.

Chengjun:  Gender, Family Characteristics and Publication Productivity among Scientists

Productivity was related to many characteristics in a survey.  The first marriage is not good for productivity, but later marriages are (maybe they marry someone already supportive of their careers), for both men and women.  Women with small children were more productive.

Kathleen: Publish or Perish?

Why people don't publish are they same reasons why they perish.  They don't think their work is worthy (or someone else thinks it's not).  It's important to be up on current literature.

Being too busy?  Publishing is difficult because there is no deadline (that's why we need this class.)

Some people are too self-critical.  Some people can't take the criticism involved in peer review.

It can be hard to organize the data.  You don't need to report all your data.

The results are not what they expect; the results are hard to explain.

"If you don't publish, the research never really happened." - Robert A. Day

Granting agencies will fund people who publish.

Andrew: Publication Productivity among Scientists: A critical review

Most people publish in their late 30s and again in their 50s or so.  This differs by discipline; some studies take longer to do.  People at major research universities publish more even if they came from less prestigious institutions.  Publishing early gets you recognition and funding to continue publishing more.  There's a positive feedback.  Personality traits that lead to high publication rates: autonomy, independence, self-sufficiency (published in 1983).

Matt:  Peer Review and the Suppression of Innovation

If peer review focuses too much on quality control, then novel approaches won't be publishes.  Peer reviewers may not be supportive of work that contradicts their past results.  The bigger journals are more conservative (in the medical field).  There are examples of papers rejected by major journals and published in minor journals that later proved to be very important.  Two Nobel prize winners were initially rejected for publication.

Ali:  Peer Review is a Two-Way Process

Peer review panels that review grant proposals are not free of bias.  Recommendations: The chair of the committee should not submit a proposal.  Reviewers should be excluded from discussion of their own proposals or proposals in which they have a conflict of interest.  Referees comments should be returned to the authors in advance of the meeting.  (I've never seen this happen.)  Promote innovation, rather than funding more of the same.  Beware of the scientist who says that "only good science should be supported."

Michaela:  How well does a journal's peer review process function?

Authors whose papers were accepted were most supportive of the review process.  Authors who were invited to resubmit found it helpful.  Authors whose papers were rejected were likely to ignore the comments!  Getting conflicting reviews was a complaint.  Timeliness was valued.  Reviewers and Editors would have a different perspective.  The emphasis should be on improving papers rather than on quality control.

Lisa:  Does Editorial Peer Review Work?  (1994)

Persistent fears about peer review: plagiarism, suppression of facts, delay of publications (by competing scientists).  Editors favor authors from famous universities, as shown by experiments sending papers to journals that had already published them, but putting unknown names as authors.  Peer review resulted in major revision of 43 of 61papers (in a medical journal); are these real improvements?  Only 10-15% of papers published on a particular topic are actually useful.  Half of all papers published are never cited.  Half of the journals on library shelves are never looked at.  Suggestions for improvement:  Less emphasis on the number of publications.

H such that h papers have been cited at least h times.

Andrew:  Drawbacks of Peer Review (an editorial in Nature)

The review process is not reproducible.  They did a survey, sending out a paper to 45 reviewers.  The results were highly variable, from excellent to unacceptable. 

Mar 26: Abstracts

Problem statement

Background

Objectives

Methods (optional)

Results

Conclusions, implications

Matt:

1. Introduces the topic
2. Hypothesis
3. Result
4. "The implications of these findings are discussed."

Michaela:

1. Introduces the topic
2. What they did (objectives)

3-4.  Descriptive statistics (results)

5-6.  Analysis of results

7. "We discuss several implications"

This abstract lists the factors that were important but doesn't give the direction of the effects.

Kathleen:

1-3.  What they did (methods).

4-5.  Results

6. Conclusion

Andrew:

1-2.  Importance.

3. Problem.
4. What they did and Results.
5. Results
6. Results and conclusion.

Pat:

1. What they did and Results.
2. Result.
3. Methods-Results-Conclusion.

Rachel:

1. What they did, objectives.

2-3.  Methods (novel method)

4-7.  Results

8-9.  Another method (model).

10. Interpretation of model result. 

Lisa:

1. Problem, suitability of these sites. 
2. Result, or could be background.
3. Objective and methods.

4-5.  Methods.  (these could have been omitted)

6-9.  Results

10-12.  Discussion (interpretation)

13. Conclusion

March 31: Proposals

Introductions can be long.  Setting up the problem statement is very important.  We need the background necessary to understand the objectives and hypotheses.

There may be other sections required by the sponsoring agency, such as "Rationale and Significance," "Justification,""Previous Work and Present Outlook."

Authors can create subheadings.  "Preliminary Supporting Data and Site Selection."  The one on judicial review had a section called "Definitions." 

Objectives

Hypotheses are very prominent.  My rule is no more than 3 Objectives, so I organize hypotheses hierarchically beneath them.

One example had boxes in the form of a flow chart, with each box explaining one objective.

The tone is very confident and definitive.  Once you get the results, it's not so tidy.

Methods sections might be called "Experimental Plan," "Procedure," "Approach," "Project Design."  You might include "Possible Pitfalls" or alternative approaches.  What problems can you foresee, and what will you do about them?

The methods might be organized to follow the objectives. 

There might be more detail on the equipment or the approach. 

Facilities and Equipment may be in an appendix.

"Continuing Education Activities and Landowner Extension and Outreach Activities."

Timeline. 

Who is doing what?  "Personnel."

Collaborative Arrangements:  Letters of support.

The sponsor may ask about "Dissemination of results", "Expected Products," Products and Outcomes," "Relevance to the funder's mission." 

Broader Impact:  NSF defines this in 5 categories.

Who is the audience for proposals?  Your proposal could be sent to ad hoc reviewers who are experts in your field.  Agencies convene panels of experts, who are assigned to review specific proposals. 

Some agencies require that your proposal not be submitted for consideration elsewhere.  Some ask that you declare where else you have submitted it.  Some do not ask.

Funding rates: 

Budget could explain what funds are currently available from other sources.

Budget Justification:  may include details of equipment requests

CVs of PIs:  If you're not publishing, then they could be afraid that the work they fund won't be published. 

Current and Pending Support: currently funded projects and those you have submitted and are awaiting a decision.

Conflict of Interest List:  co-authors from past 4 years, collaborators on research projects, thesis advisors and advisees, and consulting and financial agreements.  These people are not eligible to evaluate your proposal.

Do you write a proposal in response to a RFP (request for proposals), or do you find an RFP that matches your proposal idea?  You might add program elements to respond to stated needs.  Try to use the language and meet the spirit of the stated goals of the program. 

Page limits.  Some give guidelines as to the length of the parts.

Deadlines. 

Results of Prior NSF funding.

Response to Previous Reviews.

April 2 Writing Exercise

We discussed the capitalization of proper nouns.

Hyphenate compound adjectives:  400-L fermenter

Don't hyphenate if an adverb modifies an adjective: "naturally occurring tracers"

"0.45-um pore-size membrane", or how about a "0.45-um filter"?

How many references to cite in support of a single claim?  My rule is 3.  More makes the sentence hard to read.  And readers will not have enough guidance to know where to look.  How do you choose which to cite?  More recent papers may cite the earlier work. You may want to cite classic papers.  If you're lucky, there's a review paper.  Some papers are easier to find than others and there fore more useful.  Some are better than others.  Some are more relevant to the purpose in your paper.

Many papers cite references erroneously.  Try to be accurate.  Sometimes reviewers will notice errors and complain about them.

These are true-life examples of scientific writing: Practice improving them

Site#1 is flat and close to a stream.

The second set of samples was air dried at room temperature.

These measurements will be made every two weeks from mid-June until mid-November in the middle of a sunny day.

Farming fast-growing trees could help satisfy the increasing demand for hardwood fiber.

To produce plantation grown trees in an economically and environmentally acceptable manner, production levels and nutrient inputs must be managed.

After 42 days, plants in the amended pots had grown more than the controls.

Seedlings grew most between the fourth and fifth harvest.  Of the three species evaluated, northern red oak grew fastest.

However, when comparing the light brown class (highest in vitality) between ambient and elevated CO2 treatments, the observed means are quite different.  Mean RLD for light brown roots under ambient CO2 was observed to be between 5.98 and 8.80.  Mean RLD for light brown roots under elevated CO2 was clearly higher, with observed values between 9.12 and 11.16.

Concerns over acid deposition and forest ecosystems are expanding to the more inclusive concept of sustainable forest ecosystems.

What's wrong with this headline?  "Funding snags may sideline cutting-edge  watershed research"  Mixed metaphor. 

We were asked to identify "related policy uncertainties."

Reported increases in Pb concentration in the upper forest floor between 1966 and 1980 were also found to be an artifact of sampling technique (Friedland et al. 1984).

The fertilizer remains were sampled separately.

The first derivative of Eq. [1] is the solid-liquid phase partition coefficient (Kd), which is the dominant component of buffer power if there is appreciable interaction with the solid phase (Van Rees et al., 1990), and it is sometimes referred to as buffer capacity (Sutter et al., 1996).

Grazed permanent pasture has the potential to be an important diffuse source of P to fresh water resources (Hawkins and Scholefield 1996).

and they concluded that grassland systems on clay soils are capable of producing substantial losses of soluble phosphorus to surface waters.

LeMare and Leon (1989) found reduced P sorption with liming in an Oxisol and a Dystrochrept, but increase soption in an Andisol that contained a high amount of organic matter and allophane.

Mineral horizon tension free lysimeter solution concentrations increased over the study period.

I have found that five pages of grammatical suggestions are too many for beginners trying to punch out their first drafts, especially if English is not their mother tongue.

Clark Reservation State Park is located in Onondaga County, five miles (3.11 kilometers) southeast of the city of Syracuse, and 1 1/4 miles (0.78 Km ) west of the village of Jamesville.  It is approximately 350 acres (141.65 hectares) in size and its found at 76 05' longitude and 43 00' latitute.

The stem diameters and crown classes of the sugar maple trees sampled were similar though the mean diameter of sugar maple in the flooded zone was 27.6 cm compared to 23.2 cm from the non-flooded zone and standard deviation from the flooded zone was 7.32 cm compared to the non-flooded zone 4.39 cm. 

100 pixels for tree and grass classes respectively from each stereo pair were sampled.

Biomass of control, croptree cut, crown thinning, highgrade thinning, patch clearcut, precommercial thinning, shelterwood cut, and wildlife cut treatment is 80, 310, 181, 214, 183, 198, 291, 206, and 85 kg ha¹, respectively.

The program of events for the three-year project relative extension and continuing education activities is as follow:

 

April 9: Workshop

Chengjun: Discussion: Some other work is consistent with mine and some is not.  See if the more recent one discusses disagreement with earlier ones.

Pat:  Back to Getting Started. 

Qin:  Methods and Results: Now she has statistical results! 

Kathleen:  She made a lot of changes to the Introduction, because she had things that came up later in the paper that should have been in the Introduction.  She's worried about the new organization.

Rachel:  Three versions of the same figure.  It has a lot of information (3 ions, 3 groundwater concentrations, and streamflow and groundwater). 

Matt:  He moved some things around in the Introduction.  It should start with the theory.  (The hourglass model)

Andrew:  All the sections have changed.  The content needs to be reflected in the Introduction.

Ali brought comments from the last review.

April 13 Ethics

1. Selection of Data (Pat, Ali)

Two students have data that they can't get again (expensive and limited national lab).  They have a nice result if they can ignore two points.  We think they have to share all the information even if they don't analyze it all.  Otherwise they are bypassing the peer-review process.  If we throw out anything that doesn't fit our expectations, we aren't testing a hypothesis.

In most cases, it's not impossible to go back and try to figure out what went wrong. 

2. A conflict of interest

Two professors in the same department consult for competing biotechnology firms.  A student has a technique that could contribute to the professor that is not his advisor.  We think he should talk to his advisor before he shares what he knows.

Industrial sponsorship of academic research

Some sponsors limit the rights of researchers to publish their results.  This is not good for students.  They need to find out what the rules are.  The professor should have been more forthcoming.  Advantages: funding, relevance.  Disadvantages: not publishing.

3. Sharing of research materials

Labs invest in developing materials, strains, reagents, and then don't want to share them.  In this case, the labs have policies requiring sharing of research materials.  So the conflict might be handled at a higher level.

Credit where credit is due

What can be done when credit isn't attributed?  Ben can't gain from complaining after the fact. 

When offering to help other researchers, it can be helpful to talk about roles and authorship.  This story illustrates the drawbacks of being too generous.

4. Publication practices

What if graduate students collaborate and don't each get a first-author publication?  Some papers have notes saying that all the authors contributed equally.  They should have discussed this in advance and planned accordingly.

A career in the balance (doesn't relate well to the previous problem)

It's important to have evidence before making an accusation.  We hope that Francine's university has an equivalent of 110 Bray, where students can go for help.  It would help her to have someone to talk to, including friends outside of the lab.

5. Fabrication in a grant application.

The punishment seemed harsh, compared to the next story about plagiarism.

Ali was asking how many words in a row can be copied without quotes-he has a list of four items.  I asked him to send us the criteria for plagiarism, if he finds some.

April 21  Authorship

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

Planning

Executing

Analyzing

Interpreting

Writing

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

Ali:  Single author.  Tim Volk and Charlie Hall contributed 5 points in each of several areas.  It would be a good idea to talk to them, or maybe ask their students what they have done in other areas. 

Michaela:  Valerie had 30 points already, and she'll contribute more .  Acknowledgments:  This class, committee members, readers.  Committee members gave feedback on other chapters of the thesis, should they be authors?  Valerie might know what they expect. 

Pat:  himself, Melissa (35), Doug Allen (25).  They each got 10 points for planning, since they wrote the grant.  Acknowledgments: undergrad helpers, Eddie for stats.

Andrew:  himself, Ruth, Rene.  Adam was a graduate student who started the project and dropped out.  So he didn't have any points beyond execution.  Acknowledge field help, Eddie, funding.

Matt:  himself and Valerie.  The other members of the committee will be acknowledged (15 and 10).  Another professor who shared her class for the survey. 

Rachel: herself and Laura (MP).  John Stella became a co-MP for institutional reasons (total input 1 point).  Acknowledgments: Committee, field help. 

At this point we noted that all the author lists were the student and the MP(s), except for Ali.  This makes it seem more likely that his MP might expect to be an author.  This could be good in terms of getting more help, even if it's after the thesis is done, when the paper is prepared.

Chengjun:  5 authors:  Him, a technician (5), Nomura (23), Stipanovic (4), Nakas (23).  He put the professors in the last three positions.  Nakas wanted to be last.  Nomura ahead of Stipanovic.  Nakas suggested the order, but it could be nice to consult Nomura, who contributed a lot, to see where he would want to be.  It won't be obvious to readers that he is first in the list of professors, after someone less important.

Qin:  herself and MP (Nomura).  Acknowledgments:  the person who did the statistics, the students in the lab.

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

What about "to avoid offending"?  This could misrepresent the person's contributions, and publications are used as a measure of productivity.  It helps to identify authors and expectations as early as possible. 

Some people want to add authors to add credibility to their papers?  This doesn't seem right if they didn't contribute.  It could be a good strategy to ask such a person to contribute significantly.

What if someone makes a contribution and you don't use it?

What about paid help?  Sometimes you can get help by offering authorship in lieu of financial compensation.

6. Identify two or three internal reviewers who might be willing to read your manuscript before it is sent out to a journal (or to this class for peer review).  The fewer authors you have reading your paper, the more you need "friendly" reviewers.

Ali: Smardon, Whitney Lash offered.

Andrew:  Kevin Smith, Ralph Nyland.

Matt:  Committee members.

Rachel:  Lisa

Chengjun:  co-authors

Qin:  Greg Boyer might be good.

April 23  Abstracts

Chengjun:  He followed an example from his target journal.  Importance, objectives, conclusion.

Kathleen:  Organization.  How much detail to include in the results.

Qin:  Seems like a lot of results, needs a better conclusion.

Pat:  Should he put more numeric results?

Michaela:  Word limit is 150, it's still 100 words too long!  What should she cut?

Andrew:  Needs to cut 40 words.  He tried to include numeric results.

Rachel:  20 words over.  It takes a lot of words to describe the methods.

Lisa:  She's still working on her Discussion.

Matt:  It might be too vague, could it be more specific.  He has room for more words.

Ali:  It's within the word limit; he wants to add more specific numbers.

Kathleen:  A comparison of American and Chinese chestnut pathogen resistance using SSH to identify the impact of gene expression.  Laccase

Chinese chestnut expression of laccase compared to

Matt:  The role of mortality-related fears in determining behavior: a case study of organic food activities

Lisa:  Snowmelt events control soil and stream nitrate in winter in the Adirondacks, NY.

Andrew:  Indicators of dark heart size in sugar maple in New York State.  Difficulty in predicting or Predicting

Ali:  Slowing increase of energy return on investment of Pakistan's wheat and rice crops.

Michaela:  New York foresters' attitudes towards climate change

Qin:   Gene expression levels and PHA production by Psuedomonas putida grown on different carbon sources: glucose, glycerol, citrate, and lauric acid.

Rachel: A comparison of heat tracing and geochemical tracing estimates of groundwater discharge to Nine-Mile Creek, NY.

Chengjun:  Production and characterization of PHA from biode (computer battery died!)