Difference between revisions of "EEB 2245W"

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== Evolution 2245W-Fall 2008 ==
 
== Evolution 2245W-Fall 2008 ==
  
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'''NOTE:  For Spring 2009 EEB2245W Information, click [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB2245W-S2009 here]
  
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'''<br/>
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'''Instructor:''' Dr. Chuck Smith                                                                    '''Office:''' BioPharm 412
  
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'''Office Phone:''' 486-4158                                                                          '''Office Hours:''' By appointment
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Scientific writing advice
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• Special formatting rules apply to scientific names
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'''Email:''' smithcf@hotmail.com (Your emails to me '''MUST contain the phrase “EEB2245W” in the subject line'''; email received without that phrase, and especially those with a blank subject line, will be DELETED without being read.)
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Scientific binomials and trinomials, and genus names used alone are always italicized (or underlined).  The genus should be capitalized; the species and subspecies start in lower case.
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e.g. Homo sapiens
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Homo sapiens sapiens
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The first time the scientific name of a species is mentioned, it should be spelled out in full.  After that, the genus name is usually abbreviated (e.g. H. sapiens).
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'''Course Goals:'''  The goals of this course are to help you learn to present your ideas and arguments in clear, well-organized prose and to introduce you to library research in biology.  Because it is a science course, some of what you learn about writing will
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apply principally to scientific writing, but your efforts in this course will also translate into enhanced skills in other writing tasks.
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The assignment is geared towards writing a term paper on a subject that interests you in evolutionary biology. This is a review paper in which you will address a well-defined question of broad evolutionary significance using data from the primary literature. It is very important that you devote time and thought to your choice of topic so that you enjoy the research that goes into this paper.
  
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Higher taxonomic categories (e.g. families and phyla) are capitalized but not italicized.
 
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e.g. Chordata, Insecta, Pongidae, Plethodontidae, Scincidae
 
  
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Many taxonomic category names are also used informally (with different endings), in which case they are not capitalized.
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'''General Information:''' All assignments are due in my mailbox in TLS 312 (the EEB office) by 4 PM on the due date.  Have the secretary indicate the date and time the paper was handed in. The assignment can also be handed in personally to me. Assignments will be returned outside my office. Submit all work in computer-printed or typed form, double-spaced, with 1-inch margins and page numbers. Pay close attention to all format and length requirements.
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e.g. Not everyone is as fond of plethodontid salamanders as the author is.
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Common names should generally be capitalized (e.g. Turkey Vulture).
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'''Plagiarism:'''  Plagiarism is presenting someone else’s ideas or words as your own.  In its most blatant form, it involves quoting without quotation marks or without proper attribution of credit, including doing so from another student’s paper or from a commercially available one.  Paraphrasing without giving credit, or changing only a few words (i.e. paraphrasing too closely) even if you give credit are also examples of plagiarism.  Of course, you’ll be discussing the ideas of others in your paper, but make sure you cite the reference for each idea in the text.  The minimum penalty for plagiarism on any assignment is a 0 for the assignment.  Students who plagiarize can also be subject to more serious penalties, including failure of the course and expulsion from the University. Additional information on plagiarism is included at the end of this syllabus. You must read through the required material relating to plagiarism and sign and submit the attached form before Friday, September 5, 2008.
  
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• Write in a scientific style.  In general, discuss ideas, not “papers" or “articles”.  Do not talk about the “assignment”.  Avoid a book report style.  Write for a professional audience.
 
  
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For example, do NOT begin with a long-winded introduction:
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'''Grading notes'''
  
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Dr. Elizabeth Jockusch and Dr. Ima Nobody of the University of Connecticut published the following paper in the Journal of Evolutionary Biology: “The role of hybridization in salamander evolution.”
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1. Your grade in the W section is one quarter of your course grade in EEB 2245W. In accordance with university regulations, a failing grade for this section will result in an ‘F’ for the entire course.
  
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Appropriate would be: 
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2. 3% of the points will be deducted for each day an assignment is late up to a maximum of 15%.
  
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Jockusch and Nobody (2001) investigated how birds use their sense of smell.  
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3. Students who plagiarize or otherwise violate academic integrity are subject to serious penalties, including failure for the course.
  
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• State the authors' findings in past tense:  Jockusch and Nobody (2001) reported a general increase in researcher preferences for smelly birds.
 
  
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• Avoid excessive quotation:  In general, you should paraphrase what the authors say, not quote it, in scientific writing.  Quoting is appropriate only when the original phrasing is particularly memorable.  Unlike in some fields, where support for a claim comes from citing statements made by authorities, in science, the primary support comes from presentation of the authors' data, not of their words.  Remember that you still must use citations to give credit for the ideas, even when you are explaining them in your own words.
 
  
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• Avoid “touchy-feely” writing that relies on personal experience or feelings. Your papers should not contain the phrase "I feel that X". The important question is what you think and what you can support. (In many cases, "I feel that X" can be appropriately replaced by "I think that X" in scientific writing).
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'''sample of draft student paper, excluding conclusion:'''{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/eeb2289/EEB%202245W%20paper.pdf}}
  
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• The word “data” is the plural of “datum”.  Therefore, it is correct to say that “the data show...” not “the data shows...”.
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'''another sample of draft student paper, excluding conclusion:'''{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/eeb2289/EEB2245Wpaper2.pdf}}
  
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'''[[Details of Term Paper Assignment]]'''
  
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Additional Resources: Sugene Noh has developed a blog designed to assist 2245W students. While the blog is aimed toward students in 245W during the Spring 2008 semester, much of the information is still relevant and you are strongly encouraged to look at what Sugene has posted. The blog may be accessed at:
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'''[[Organization of the paper]]'''
  
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http://uconnwritinginscience.wordpress.com/
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'''[[Here’s a useful (and amusing) example, put together by Dr. Kurt Schwenk, to get you thinking about how to cite references]]:
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'''
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The UConn writing center (http://www.writingcenter.uconn.edu/) is available to provide additional help at all stages in the writing and revising process. They provide individual tutors to work with you (it's free), and the past experience of EEB 2245W students has been very positive.
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[[Schedule and Deadlines]]
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Sep. 5 (Friday) Decide upon your topic & get my approval
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Sep. 12 (Friday)    Introduction due (2-3 pages). Remember to include a Literature Cited section for references cited in your Introduction.
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Sep. 15-19 Individual meetings with me (to be arranged); discuss Introduction. (I), then revise it.
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'''[[Tips for Getting Started]]'''
  
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Sep. 25  (Thursday) Revised Introduction due; First half of main text due (~5-6 more pages). Remember to update your  Literature Cited section for references added in the first half of the main text.
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'''[[Writing Tips]]'''
  
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Oct 7 (Tuesday) Second half of main text due (~5-6 more pages). Remember to update your  Literature Cited section for references added in the second half of the main text.
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'''[[General rules for citing sources in scientific writing]]
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'''
 
   
 
   
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Oct 20-24. Individual meetings with me (to be arranged); discuss main text.
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'''[[Scientific writing advice]]'''
  
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Nov 13 (Thursday) Abstract (new), Introduction, main text (both revised) and Conclusions (new) due. The result must be a complete paper in the required format, including a Literature Cited section. This must NOT be a draft, not even a final draft, but a paper you have thoroughly edited and proofread. It must reflect a major effort on your part to produce a polished final paper. You will be graded on the extent to which you have reached this ideal.
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'''[[Schedule and Deadlines]]''' '''and Grading Scheme'''
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Nov 20 (Thursday Comments on the first version of your Conclusions section will be returned.
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Dec 4  (Thursday) Final complete revised paper due.
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'''[[Possible Term Paper Topics]]'''
  
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Grading breakdown (100 point scale)
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'''[[Policy on Plagiarism]]'''
  
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'''Additional Resources:'''
  
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To be determined
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Sugene Noh has developed a blog designed to assist 2245W students. While the blog is aimed toward students in 245W during the Spring 2008 semester, much of the information is still relevant and you are strongly encouraged to look at what Sugene has posted. The blog may be accessed at:
  
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http://uconnwritinginscience.wordpress.com/
  
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The UConn writing center (http://www.writingcenter.uconn.edu/)  is available to provide additional help at all stages in the writing and revising process.  They provide individual tutors to work with you (it's free), and the past experience of EEB 2245W students has been very positive.
  
  
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'''Grading breakdown (100 point scale)'''
  
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[[Possible Term Paper Topics]]
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To be determined
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Below are some examples of possible evolution term paper topics.  You are encouraged to come up with your own topic.  You will be spending a significant amount of time researching and writing about the topic you have chosen this semester, so it is important to choose a topic that interests you.
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Examples of term paper topics
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1. The evolutionary origin of a group of organisms such as angiosperms.
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2. Do parasites become less deleterious to their hosts over evolutionary time?
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3. How important was human activity in the major extinctions of the Pleistocene?
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4. Evidence for Cope's Rule.
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5. An evolutionary tendency in insular animals (e.g. smaller mammals, gigantism, or flightlessness).
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6. The molecular basis for reproductive isolation
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7. The evolutionary significance of introns.
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8. The evolution of altruistic behavior.
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9. The role of evolutionary change in the success of invasive species
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10. Evolutionary response to climate change
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11. The evolution of eusociality in insects and mammals.
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12. How did flight evolve in birds or insects?
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13. Adaptive vs. nonadaptive radiations
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14. The evolutionary significance of hybridization
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[[Policy on Plagiarism]]
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Plagiarizism is defined as  "To take something (ideas, writings, etc.) from anyone and pass them off as one's own" (Webster's New World Dictionary, 2nd Ed., 1976).  Often students are not clear on what constitutes plagiarism. 
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Here are some common examples: 
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• Copying another student's work (whole or part) is plagiarism.
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• Failure to give full and proper citation to other individual's published work is plagiarism.
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“Full and proper citation” requires the following:  (1) quotation marks around any quoted passage , (2) a correct citation to the publication from where the ideas originated in the text, and (3) a complete reference to that publication in the "Literature Cited" section of a formal paper or assignment.  If an author’s work is paraphrased, then quotes are not needed, but the idea must still be followed by a correct citation in the text and a complete reference to that publication in the “Literature Cited.” This applies to all forms of communication including websites, textbooks, lab manuals, or even a personal communication from someone. Plagiarism is a serious violation, as stipulated in the Academic Misconduct section of “The Student Code” at the University of Connecticut, and it will not be tolerated in this course.  You are to familiarize yourself with University’s policy on Academic Misconduct at the following web address: http://www.dosa.uconn.edu/student_code.html
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The instructors of this course will adhere to the guidelines outlined in “The Student Code,” therefore students should read and understand these policies and the consequences of such violations.
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There are many resources available to students to help illustrate plagiarism including the websites listed below.  It is your responsibility to become fully informed about this issue. You should spend as much time as is necessary to visit each of these websites and become familiar with the material on plagiarism presented on the sites before September 5, 2008. You should then sign the page below and turn the sign paper into your writing instructor before September 5, 2008. Your signature on this paper signifies that you understand what constitutes plagiarism, that you have read the required information, and that you agree to abide by the University of Connecticut Code of Student Conduct.
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http://owl.english.purdue.edu/handouts/print/research/r_plagiar.html
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http://www.indiana.edu/~wts/pamphlets/plagiarism.shtml
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http://www.northwestern.edu/uacc/plagiar.html
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I have read and understand this document ______________________________    ________________
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            Signature Date
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EEB 2245W-Plagiarism Example
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The following paragraph comes from this review article:
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Van Dover C. L., C. R. German, K. G. Speer, L. M. Parson. and R. C. Vrijenhoek.  2002.  Evolution and biogeography of deep-sea vent and seep invertebrates.  Science 295:1253-7.
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“Since 1977, taxonomists have described more than 400 morphological species from vents (7) and 200 more from seeps (6). This corresponds to a species description every 2 weeks throughout the past 25 years. Some vent and seep invertebrate species are immigrants from the surrounding deep sea, whereas others may be derived from shallow-water species. Many of the invertebrate taxa found at vents and seeps have undergone evolutionary radiations at the species level (7). Other species have a longer history of endemicity, having diversified within vent and seep habitats at generic, familial, and higher ranks. Where high taxonomic levels of endemism are observed, origins may be ancient, extending back to the Paleozoic [540 to 248 million years ago (Ma)] (8). Genera of stalked barnacles and a superfamily of primitive gastropods endemic to vents are thought to be Mesozoic (245 to 65 Ma) relics or living fossils (8, 9). Chemosynthetic environments have thus been posited as stable refugia from global extinction events that devastated biological diversity in euphotic zones (7, 10).”
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Here’s a paragraph from a student’s term paper:
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The evolutionary history of vent and seep faunas dates back millions of years, providing ample time for adaptation and speciation. Since the discovery of these chemoautrophic communities, more 400 species have been identified at vents, along with over 200 at seeps (Van Dover et al, 2002). Many of these organisms are the derivations of ancient deep sea organisms that migrated into the habitats, while others migrated in from shallower water. While these organisms entered vents and seeps from the surrounding waters and speciated into some of the modern vent and seep invertebrates, many other species are believed to have been endemic to vents or seeps for a much longer time. Fossil evidence suggests that many endemic species in vents and seeps may have existed in the Paleozoic Era (540 to 248 million years ago). Meanwhile, other endemic species such as stalked barnacles and primitive gastropods are thought to date back to the Mesozoic (245 to 65 million years ago). (Van Dover et al, 2002). Given the age of these fossils, it is safe to say that vents and seeps formed a safe-haven for organisms during events of mass global extinction, such as that which wiped out the dinosaurs 65 million years ago as well as many organisms that may have been living in shallower wat
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[[Category:EEB Courses]]
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Latest revision as of 01:08, 21 January 2010

Evolution 2245W-Fall 2008

NOTE: For Spring 2009 EEB2245W Information, click here


Instructor: Dr. Chuck Smith Office: BioPharm 412

Office Phone: 486-4158 Office Hours: By appointment

Email: smithcf@hotmail.com (Your emails to me MUST contain the phrase “EEB2245W” in the subject line; email received without that phrase, and especially those with a blank subject line, will be DELETED without being read.)


Course Goals: The goals of this course are to help you learn to present your ideas and arguments in clear, well-organized prose and to introduce you to library research in biology. Because it is a science course, some of what you learn about writing will apply principally to scientific writing, but your efforts in this course will also translate into enhanced skills in other writing tasks. The assignment is geared towards writing a term paper on a subject that interests you in evolutionary biology. This is a review paper in which you will address a well-defined question of broad evolutionary significance using data from the primary literature. It is very important that you devote time and thought to your choice of topic so that you enjoy the research that goes into this paper.


General Information: All assignments are due in my mailbox in TLS 312 (the EEB office) by 4 PM on the due date. Have the secretary indicate the date and time the paper was handed in. The assignment can also be handed in personally to me. Assignments will be returned outside my office. Submit all work in computer-printed or typed form, double-spaced, with 1-inch margins and page numbers. Pay close attention to all format and length requirements.

Plagiarism: Plagiarism is presenting someone else’s ideas or words as your own. In its most blatant form, it involves quoting without quotation marks or without proper attribution of credit, including doing so from another student’s paper or from a commercially available one. Paraphrasing without giving credit, or changing only a few words (i.e. paraphrasing too closely) even if you give credit are also examples of plagiarism. Of course, you’ll be discussing the ideas of others in your paper, but make sure you cite the reference for each idea in the text. The minimum penalty for plagiarism on any assignment is a 0 for the assignment. Students who plagiarize can also be subject to more serious penalties, including failure of the course and expulsion from the University. Additional information on plagiarism is included at the end of this syllabus. You must read through the required material relating to plagiarism and sign and submit the attached form before Friday, September 5, 2008.


Grading notes

1. Your grade in the W section is one quarter of your course grade in EEB 2245W. In accordance with university regulations, a failing grade for this section will result in an ‘F’ for the entire course.

2. 3% of the points will be deducted for each day an assignment is late up to a maximum of 15%.

3. Students who plagiarize or otherwise violate academic integrity are subject to serious penalties, including failure for the course.


sample of draft student paper, excluding conclusion:Pdficon small.gif

another sample of draft student paper, excluding conclusion:Pdficon small.gif

Details of Term Paper Assignment

Organization of the paper

Here’s a useful (and amusing) example, put together by Dr. Kurt Schwenk, to get you thinking about how to cite references:

Tips for Getting Started

Writing Tips

General rules for citing sources in scientific writing

Scientific writing advice

Schedule and Deadlines and Grading Scheme

Possible Term Paper Topics

Policy on Plagiarism

Additional Resources:

Sugene Noh has developed a blog designed to assist 2245W students. While the blog is aimed toward students in 245W during the Spring 2008 semester, much of the information is still relevant and you are strongly encouraged to look at what Sugene has posted. The blog may be accessed at:

http://uconnwritinginscience.wordpress.com/

The UConn writing center (http://www.writingcenter.uconn.edu/) is available to provide additional help at all stages in the writing and revising process. They provide individual tutors to work with you (it's free), and the past experience of EEB 2245W students has been very positive.


Grading breakdown (100 point scale)

To be determined

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