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NR 495 Fall 2008
Liz Harp
Office: E208 Anatomy/Zoology
Email: 
eharp - at - lamar.colostate.edu

Students:


Field Crew

Flea Identification

Field and Lab

Allison Fockler

Courtney Younginger

David Yoo

Jackie Wheeler

Tori Wheeler
Beckie Blaskovich

Peggy Tormohlen

 

 

 

 

Alycia Nelson

Nathan Marsteller

Sarah Legare

Student schedules

Important Information

 

NEXT LAB MEETING: Friday, December 5, 4:00pm
Anatomy/Zoology E112
This will be the final run-through of your presentations before the "official" presentations the following week (this might take 2-3 hours - please plan accordingly).  Your presentations should be in final form by today for an uninterrupted run-through.  Pay close attention to time - it will be a significant part of your grade.  Your ability to present the information will also be a significant part of your grade.  Make sure that your presentations tell a coherent story, and that they will be interesting and accessible to a diverse audience (e.g., plant ecologists, biogeochemists, wildlife ecologists, various academic levels).

Click here for a copy of the presentation I used at a meeting in July - this should help with both your papers and presentations.  Feel free to use any of the pictures/figures in your presentations.  I think the presentation has issues with versions of MS Office earlier than 2007 - mostly with pictures overlapping the text.  Which reminds me, if you are using Office 2007, make sure you (1) save your presentation in *.ppt format, and (2) you test it on a machine that does not have Office 2007.

Final paper due Friday, November 14, 2:00pm via email.  Please send your paper in *.doc or *docx format, along with PDFs for references you use and for which you have not already sent PDFs 

Journal abbreviation resources on the web:
http://library.caltech.edu/reference/abbreviations/  
http://www.library.uiuc.edu/biotech/j-abbrev.html  
http://www.lib.umd.edu/guides/scijrnl.html  

Some things I've noticed in your seminar write-ups, and from student papers in the past, that you will want to be careful about in your papers (I will add to this as I remember/notice more issues, so please check back often!):

The difference between affect and effect
http://grammar.quickanddirtytips.com/affect-versus-effect.aspx

Use of the word "the"
This is one of the most overused words in many papers - use the "find" function in Word to find every instance of "the, and make absolutely sure that it is necessary.  For instance, "the plague" should usually just be "plague", and "the prairie dog" should usually just be "prairie dogs".  

Plural vs singular: data
Data is plural - make sure to use the correct verb when you use it in a sentence.
For example "...when the data is entered..." should be "...when the data are entered..."
Here's a good site for some other things to look out for in science writing:
     http://lasi.lynchburg.edu/benson_k/public/writing/writing.html

Some good advice about proofreading: 
http://grammar.quickanddirtytips.com/proofreading.aspx

I haven't read the whole page, but at first glance this looks like a good reference:
http://en.wikipedia.org/wiki/Scientific_writing

Click here for some definitions of words that I found commonly misused or obviously misunderstood in your papers

 

     
Important
Documents
  Syllabus

Seminar write-up guidelines

Paper grading criteria

Some pointers about layout and content for your paper

Presentation grading criteria (coming soon)  
     Here's the presentation grading criteria from Spring 2008 - yours will look pretty similar to this

     
Seminar
Links
   Biology

 Biomedical Sciences

 Cell & Molecular Biology

 College of Vet Medicine and BioMed Sciences

 Colloquium in the Life Sciences

 Clinical Sciences

 Environmental and Radiological Health Sciences

 Fisheries, Wildlife, and Conservation Biology
   

Forest, Rangeland, and Watershed Stewardship

Geosciences

Graduate Degree Program in Ecology

Human Dimensions of Natural Resources

Horticulture and Landscape Architecture

Microbiology, Immunology, & Pathology

Molecular, Cellular, and Integrative Neurosciences

Soil and Crop Sciences

Physiology

 

     
Required Reading:   Work through the following tutorials by Tuesday, September 2nd

How to find articles (CSU library "how to" page)

How to Use ILLiad (CSU library tutorial)

Beginning Boolean Searching (CSU library tutorial)

Advanced Boolean Searching (CSU library tutorial)

Web of Science Tutorial

EndNote X2 Tutorial (click on the link near the top: "EndNote X2 Tutorials")
(if you don't have EndNote, then just read through this one to get an idea of what EndNote is for and how it can help you)

Read the following by Friday, September 5th

Hoogland, John L. (1995) The Black-Tailed Prairie Dog: Social Life of a Burrowing Mammal. (chapters 1 & 2)

Hoogland, John L. (1996) Cynomys ludovicianus. Mammalian Species. 535:1-10
(find this article on the Mammalian Species page - click here)

Read the following by Monday, September 8th

Little, John W. and R. Parker (2005) How to read a scientific paper

How to interpret graphs and tables (this is short, but very important)

 

     
Paper Assignment   Your paper will be in the format of a proposed research essay for the NSF Graduate Research Fellowship, with the exception that you will use "we" instead of "I" when referring to what will be done and what has already been done.  Your paper should be 4 pages, double-spaced, 1" margins, 12 point Times New Roman (or 11 point Calibri if you are using Word 2007).  I'm always a bit shocked when people lose points because they didn't format correctly.  Please pay attention to the formatting requirements on the grading sheet.

Some helpful websites:

http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=6201

http://www.nsf.gov/pubs/2007/nsf07576/nsf07576.htm

https://webspace.utexas.edu/moontj/IMPACT/NSF/index.htm

http://rachelcsmith.com/NSF.html

http://ctl.stanford.edu/Tomprof/postings/730.html

http://www.training.nih.gov/trainees/documents/nsfgrfp.pdf

Note that the proposed research essay is only a small part of the entire NSF Graduate Research Fellowship application.  I encourage you to familiarize yourself with the application if you are planning to go to graduate school - it's a great fellowship, and very prestigious.  However, for this assignment, you will only be paying attention to the proposed research portion of the application.  Pay particular attention to the criteria for "Intellectual Merit" and "Broader Impacts".

Your proposed research paper must be for the prairie dog project, and will need to include an introduction to the problem (i.e., why it is important, and what has already been done), explicit hypotheses, brief study design, anticipated results, and explicit intellectual merit and broader impacts sections  (see the NSF site for explanations of these).

All of your references (with the exception of the Hoogland book - see below) will need to be from scientific journals.  This means no websites, books, magazines, newspapers, etc.  The safest way to make sure you are using appropriate references is to use Web of Science to find all of your references.  Note that most scientific journals post their journal content online in the form of PDFs, and CSU has quite a few electronic subscriptions to these journals - it is perfectly fine, and in fact encouraged, to find the articles online.  There is actually  no reason for you to have to visit the library for this paper, particularly since you will need to email me PDFs of all of the references that you use in your paper.  The CSU library is happy to obtain PDF copies of journal articles when we don't have an online subscription to a specific journal, or if our subscription does not cover the issue that your reference is in (not all years are always available electronically).  

Try to find the articles in the list of suggested references (below) before our first lab meeting, so that I can answer any questions you have before it is an emergency.

I strongly suggest using EndNote bibliographic software... if you've never used it, I'm happy to set up a group time when we can go over why it's useful and how to use it (also see the tutorial that is required "reading").  You can purchase EndNote for a very reasonable price (~$99 with the academic discount) at the Software Cellar in the Lory Student Center.  Freshman and Sophomore students are always grateful to have discovered EndNote early in their academic careers, and Junior and Senior students always wish they had discovered it sooner.  Each of my students who have used it have been grateful to have had it.

Some words of advice... don't wait until the last minute to write your paper!  All sorts of things can go wrong at the last minute (usually computer related), and I will almost certainly be able to tell that you threw it together without much thought, and there will be a resulting loss of points.  Most importantly, you will probably have to order at least one or two articles via interlibrary loan, and this can sometimes take a week or more!  At the very least, get started on the outline of the paper and think about what references you want to use as soon as possible so that you can order them well in advance of when you need them.  There is also a good possibility that I will not be available at the last minute (i.e., the day before and the day of the due date) to answer your questions... I am happy to answer questions in advance of the due date - it's not a test - you can ask as many questions as you want, though please try to be thoughtful about your questions - it is going to be a very busy semester for me.

     
Useful websites   http://grammar.ccc.commnet.edu/GRAMMAR/plague.htm

http://grammar.quickanddirtytips.com/affect-versus-effect.aspx

http://grammar.quickanddirtytips.com/proofreading.aspx

http://en.wikipedia.org/wiki/Scientific_writing

     
Helpful articles and resources:  

Antolin, M. F., P. Gober, B. Luce, D. E. Biggins, W. E. Van Pelt, D. B. Seery, M. Lockhart, and M. Ball. 2002. The influence of sylvatic plague on North American wildlife at the landscape level, with special emphasis on black-footed ferret and prairie dog conservation. Transactions of the North American Wildlife and Natural Resources Conference 67:104-127.

Acevedo-Whitehouse, K., and A. A. Cunningham. 2006. Is MHC enough for understanding wildlife immunogenetics? Trends in Ecology & Evolution 21:433-438.

Altizer, S., D. Harvell, and E. Friedle. 2003. Rapid evolutionary dynamics and disease threats to biodiversity. Trends in Ecology & Evolution 18 (11):589-596.

Daszak, P., A. A. Cunningham, and A. D. Hyatt. 2000. Emerging infectious diseases of wildlife: threats to biodiversity and human health. Science 287:443-449.

Frankham (2005) Genetics and extinction. Biological Conservation 126:131-140

Hoogland, J. L. 1995. The Black-Tailed Prairie Dog: Social Life of a Burrowing Mammal. Chicago: University of Chicago Press.  (this is the one exception to using journal articles for your paper - you may use this book, but this is the only non-journal source you may use)

Kotliar, N. B. 2000. Application of the new keystone-species concept to prairie dogs: How well does it work? Conservation Biology 14 (6):1715-1721.

Miller, B. J. et al (2007) Prairie dogs: an ecological review and current biopolitics.  The Journal of Wildlife Management. 71:2801-2810

Piertney, S. B., and M. K. Oliver. 2006. The evolutionary ecology of the major histocompatibility complex. Heredity 96 (1):7-21.

Schwartz, M. K., G. Luikart, and R. S. Waples (2007) Genetic monitoring as a promising tool for conservation management. Trends in Ecology and Evolution. 22:25-33

Sommer, S. 2005. The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Frontiers in Zoology 2:16.

     
Lab Meeting Dates and Times*

* subject to change

  Friday, September 5, 4:00pm:  We will discuss the requirements of the course and talk about what is involved in each project.  We will also discuss the required reading due this week.  Please bring questions.  A lack of questions is usually a sign that you did not do the reading, or did it at the last minute, and this will be noted.  If I can remember my camera, we'll take a group picture today.

Friday, September 12, 4:00pm:  We will discuss the paper assignment and the required reading.  Please  bring questions.  See note about lack of questions above.

Friday, September 26, 4:00pm:  Give serious thought to your paper before this date -  it will be your best chance to ask any questions you have before your first submission is due Friday, October 3.  By now you should have most of the articles you will use in PDF form, and at the very least, an outline of your paper.

Friday, October 10, 4:00pm: You will need a rough draft or outline of your presentation before this date - this well be your best chance to ask any questions you have before your presentation is due October 13

Friday, October 17, 4:00pm: We will talk about your papers and presentations - bring questions.

Friday, November 7, 4:00pm: Your presentations should be in "final form" by today for an uninterrupted run-through.  Pay close attention to time - it will be a significant part of your grade.  (this might take a couple of hours - please plan accordingly)

Friday, December 5, 4:00pm: The final run-through of the presentations before the "official" presentations the following week (this might take a couple of hours - please plan accordingly)

     
Assignment tracking   I will mark on the website when you have received credit for an assignment.  In the interest of privacy, I will not post grades with your name.

Please send your papers and seminar write-ups via email in an attached Word doc.
Please remember to send all pdfs with your papers.

  Hours
Total*
Sem.
1
Sem.
2
Sem.
3
Sem.
4
Sem.
5
Paper
1**
Paper
2**
Final Paper Pres.
Draft
Practice
Pres.
1
Practice
Pres.
2
Final
Pres
Lab
Mtg
1
Lab
Mtg
2
Lab
Mtg
3
Lab
Mtg
4
Lab
Mtg
5
Lab
Mtg
6
Lab
Mtg
7
 
DUE  >>> Dec
5
Sept
19*
Oct
3*
Oct
17*
Oct
31*
Nov
14*
Oct
3*
Oct
24*
Nov
14*
Oct
17*
Nov
7*
Dec
5*
Dec
12
Sept
5
Sept
12
Sept
26
Oct
10
Oct
17
Nov
7
Dec
5
 
proportion of category   20% 20% 20% 20% 20% 20% 30% 50% 10% 15% 25% 50% each missed lab meeting will negatively affect your final grade -
exact impact to be decided, but it will not be trivial
high grade     100 100 100 100   98 105   100 77                    
avg grade    100 100 100 100   69 71   100 65                    
Date: Nov
14
                                       
Allison
(26)
102:00 x x x x x x x x x x     X X X x x x    
Alycia 82:05 x x x x x x x x x x     X X X x x x    
Beckie
(26)
63:10 X x x x x x x x x x     X X X x x x    
Courtney 91:35 x x x x   x x x x x     X X X x absent x    
David 85:55 x x x x x x x x   X X X x x x    
Jackie 84:00 x x x x   x x x x x     X X X x x x    
Nathan 104:10 X x x x   x x x x x     X X X x x x    
Peggy 80:15 x x x x x x x x x x     X X X x x x    
Sarah
(96)
193:10 X x x x x x x x x x     X X X x x x    
Tori
(37)
90:45 x x x     x x x x x     X absent x x absent x    
                     
Paul <-27>  
                     
    ** I have planned for you to have three "chances" to turn in your grant proposals, however, if on the first or second submission you receive a 95% or better, you do not need to turn in additional submissions.  

* There will be a 5% penalty per day for assignments handed in after the due date and time.
   

    * in order to stay on track for finishing your hours by mid-November, these are general goals you should shoot for:
Date: Sept 12 Sept 19 Sept 26 Oct 3 Oct 10 Oct 17 Oct 24 Oct 31 Nov 7 Nov 14
Lab & field 22 hrs 30 hrs 38 hrs 45 hrs 53 hrs 60 hrs 68 hrs 75 hrs 83 hrs 90 hrs
Field only 25 hrs 34 hrs 43 hrs 52 hrs 61 hrs 70 hrs 79 hrs 88 hrs 90 hrs 90 hrs
Sarah Legare
(180 hrs for 4 credits)
112 hrs 120 hrs 128 hrs 135 hrs 143 hrs 150 hrs 158 hrs 165 hrs 173 hrs 180 hrs

If you get a little behind in your hours, and need to make up some hours to stay on track, there are opportunities for data entry, fixing traps, and general lab duties.  You can also get 2 hours of credit for attending a Science Cafe - these are the 2nd Wednesday of every month at 5:30pm downtown at the Starry Night Cafe.  Other opportunities are listed below. 

To get 2 hours credit for attending a Science Cafe, please send me a couple of paragraphs about what generally the speaker talked about (just a couple of sentences or so on this), what the most interesting things you learned were, and what you liked and didn't like about the presentation in general.

More info on Science Cafe here: http://beetstreet.org/Science-Cafe 

To get 1 hour of credit each for attending one or more of events listed below, please send me a couple of paragraphs about what generally the speaker talked about (just a couple of sentences or so on this), what the most interesting things you learned were, and what you liked and didn't like about the presentation in general.

Preeminent Field Biologist George Schaller
September 29, 2008, 05:00 PM, Clark A103

A Life in the Wild: A Conversation with George Schaller
Simucast to be held in Clark
Join preeminent field biologist George B. Schaller, recipient of the 2008 Indianapolis Prize, for an interview and question-and-answer simulcast, live on select PBS stations and webcast to Colorado State University.
    More details online:
    http://events.colostate.edu/event_view.asp?EID=23369

     
 
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