introduction

4

BIOL 3251 Writing Assignment 2 – Introduction and Hypothesis

The entirety of the assignment is to help you construct polished and professional text for the introduction and hypothesis (red rectange] that you can use for your poster. You will get feedback from peers and your instructor. All parts of this assignment should be uploaded to the Writing Assignment 2 Dropbox on D2L.

Initial Draft

· This should be about 1 typed page, not including Literature Cited or any figures (diagrams or graphs).

· Your initial draft is due at Sunday June 15 at 9:00PM . Submit it to 2 places: D2L dropbox for writing assignment 2 and Discussion – Poster Introductions You will have to post your intro before you can review other’s.

· A rubric for this assignment is available on the Dropbox folder and the Grades section.

1. Begin by taking out a sheet of paper and brainstorming for 90 seconds. Scribble down everything you can think of about the gene, topic, treatment you’ve chosen – write down everything you can think of!!!

If you are struggling for ideas, in your initial NCBI search for your gene of interest, under the results by database, you may have seen “OMIM” This is the Online Mendelian Inheritance in Man database, and may link your gene of interest to human disease or conditions.

2. Now take a look at your brainstorm. Use circles or highlighter colors to group the words/concepts into broad groups. What broad concept or topic group could you use to get other people (your audience) interested in your topic? Begin with a 2-3 sentences about that broader topic or concept.

This section, and those that follow, also need references for any facts or concepts that are not common knowledge. If you have to look it up, it needs a reference. If a paper can be referenced in a journal, use that. Only use web addresses when there is no other source. Make sure you use “in text” citations AND a Literature Cited section according to the CSE style (name-year). Remember, you can visit the Writing Center for help on style and/or writing!

Example of “In text” citation for an introductory document:

F. psychrophilum is a pathogenic organism responsible for causing severe diseases in Oncorhynchus mykiss, rainbow trout (Rochat et al. 2017).  This pathogen causes detrimental effects, including skin and muscle degeneration, to rainbow trout populations (Henriksen et al. 2014).

Literature Cited

Henriksen MMM, Madsen L, Dalsgaard I. 2013. Effect of Hydrogen Peroxide on Immersion Challenge of Rainbow Trout Fry with Flavobacterium psychrophilum. PLoS ONE 8(4):35-42.

Rochat T, Fujiwara-Nagata E, Calvez S, Dalsgaard I, Madsen L, Calteau A, Lunazzi A, Nicolas P, Wiklund T, Bernardet J-F, et al. 2017. Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme. Frontiers in Microbiology 8(2):236-238.

3. Use the next 4-5 sentences to bring in some relevant, but more scientific facts and details that your reader/audience might want to know. Also consider which facts and/or concept that will be necessary for a reader/audience to know to be able to understand the more detailed information that comes next. You should pick facts supported in the literature you’ve been gathering.

4. Now, use the next 4-5 sentences to begin to draw the reader into the very fine details… you want to lead them into being very focused on your specific question/hypothesis (item 7).

5. Make sure you have included reasonable transitions between ideas and concepts above – that is, you need the text to flow smoothly from one topic to the next, rather than jumping from one idea to another. Help your reader out; they are a newbie to this!!!!

6. Are there images or graphs that you might add to aid in drawing interest or making an idea easier to understand? For a poster, which is our final goal, you can use images and drawings from papers in your introduction, but you must cite them in a figure legend and put the citation in your Literature Cited section. Please note that this is different for a document you want to publish, where you cannot use any art or images from others without their official permission.

Example:

Figure 1. C. elegans Life Cycle. Life stages are designated as names outside the double ring. Color coding within the rings corresponds to the timing of the life stage. Times are listed in hours. Larval stages 1 thru 4 are noted as L1, L2, L3, and L4, respectively. (image from Blaxter 2010).

Literature Cited

Mark Blaxter’s Teaching Pages [Internet]. 2010. Version 4.01. Edinburgh: Mark Blaxter; [updated August 2019; cited August 2019]. Available from: http://www.nematodes.org/teaching/tutorials/Caenorhabditis/caenorhabditis_lifecycle.shtml .

7. You’ll want to end with your hypothesis statement. Our experiment is more “hypothesis-generating” than hypothesis-testing. If we were in the lab, we could do more direct testing of a hypothesis. If your background information has led to a testable hypothesis, great! If not, you can describe the search that you are undertaking. Remember, we can only use online bioinformatics databases for our projects, and we have not explored many tools yet, so your statement may be limited.

How can you phrase this question as a hypothesis statement, being very specific to your selected gene the resources that we areusing? Be careful to address only what your experiment is actually testing. See below and the printed page from Science Buddies (https://www.sciencebuddies.org/blog/a-strong-hypothesis) that has examples of hypothesis statement that are of different quality.

Example of too broad and not specific: The alternative splicing in this gene should show exactly where the splicing is occurring and exactly how this gene helps with the development, and what exactly can go wrong.

Revised: RNA from the Fox2P gene will be alternatively spliced to form different isoforms in regions of the human brain associated with vocal development (amygdala, cerebellum) compared to those not associated with vocal development (basal ganglia) as measured by reverse transcription-polymerase chain reaction.

Avoiding Plagiarism

Now that you're beginning to write your introduction and hypothesis, it is important that you are careful to avoid plagiarism. Plagiarism is when you use another person's words, ideas, images, or data without giving them credit.  Plagiarism has several "flavors" or types (see below and the black square in the image below).  We generally see beginning science students make 3 types of mistakes that are plagiarism. 

1. Plagiarism types 1 and 2 (aka direct plagiarism): This is when a writer DIRECTLY copies the words from another source.  This is plagiarism whether you cite it (type 1) or not (type 2).  Direct copying is NEVER ok.  Technically, you could use quotes and cite the author, but in science, we RARELY quote - we summarize and/or paraphrase.  We know it can be difficult to put these complex ideas into your own words, but you must find a way to begin using your voice. 

2. Plagiarism type 3 (aka paraphrasing without citation): This is when a writer summarizes or paraphrases the ideas from another source, but doesn't cite the source.  If an idea, image, etc is NOT YOURS, you must cite it.

This webpage at Northern Illinois University (https://www.niu.edu/academic-integrity/students/plagiarism/index.shtml) has very good information about plagiarism with examples of all the different kinds (links are in the black square) and tips for avoiding plagiarism (black arrow).

3. To help you and us, we have turned on your ability to see the "turnitit" report to see the similarity score and report for your documents.  You can view this by going to the dropbox and clicking on your document.  From there you will see a similarity score and can click on it to see the parts of your paper that matched known sources EXACTLY.  We expect some similarity based on commonly used words and you can go here to see a bit more about interpretation, generally: https://help.turnitin.com/feedback-studio/turnitin-website/student/the-similarity-report/interpreting-the-similarity-report.htm.

Color Scoring System Interpretation

A green score  (0- 24%) indicates a percentage that is acceptable and within the range of just random match due to common words.

A yellow score (25-49%) indicates a percentage that may or may not indicate some plagiarism.  To interpret this one, take a look at the blocks of similarity.  If large sections of text are exact matches (more than 4 words in a row; see below), you will want to re-word this section IN YOUR OWN WORDS. 

Source: https://oit.colorado.edu/services/teaching-learning-applications/turnitin-plagiarism-protection

Source: https://www.brad.ac.uk/elearning/Plagiarism/Student-Guide-to-TurnitinUK/page_08.htm

If the blocks are small (less than 4 words in a row), this is acceptable.  It is possible that the similarity score is high because it is finding your references as "blocks of identity;" this is also acceptable.

An orange score (50-74%) means a lot of text was found to be an EXACT match to other sources (see above).  This is NOT acceptable - you need to use your own words!  We know that re-wording complex scientific concepts can be hard, but you have to start using your own voice.  CAUTION: Again, it is possible, though less likely here, that the similarity score is high because it is finding your references as "blocks of identity;" this is also acceptable.

A red score (75%-100%) means that most of your text was found to be an EXACT match to other sources (see above). This is NOT acceptable - you need to use your own words! We know that re-wording complex scientific concepts can be hard, but you have to start using your own voice.

4. If you find that you have too much similarity, simply fix it and upload a new document to the same dropbox. If you are concerned or have trouble, visit either: 1. one of us in the Tutoring Spot or 2. the Writing Center to discuss.  Our Tutoring Spot hours are in the syllabus and a Writing Center appointment can be made here: https://www.mtsu.edu/writing-center/.  The UWC is open every day except Saturday. We can see the submission dates and time and will only look at the last submission.

5. We look very closely at all papers having yellow or higher scores.  If your instructor finds that your paper has plagiarism, that is unacceptable EXACT match(es) overall OR a even single large block, we will have to refer this to the Office for Academic Misconduct.  The consequences are noted in your syllabus.  We do not want to have to take this option with ANYONE, but we have ethical standards to uphold, too.

Checklist

x	What	Where	When
	Initial Draft	· D2L Dropbox (Writing Assignment 2) and · Peer discussion posting in D2L	By Sunday 6/15 6/14 at 9:00PM
	Peer Review for Others	· Review the work of 3 other students in class	By noon, Tuesday 6/17 6/16
	Rebuttal Letter and revised draft	· D2L Dropbox (Writing Assignment 2)	By 9:00PM, Thursday, 6/19 6/18
	Final version I will see your FINAL version on your poster.	· D2L Dropbox (Writing Assignment 2)	By 9:00 PM, Saturday 6/21 6/20

Peer Review

Reviewing the work of others helps them, but it also helps you to see how you can write better as well. You can read more about peer review in learning here: https://serc.carleton.edu/sp/library/peerreview/what.html

General Guide to Peer Review

· Before you even make your first comment, read the document all the way through.

· Point out the strengths as well as the weaknesses of the document.

· Offer suggestions, not commands.

· Editorial comments should be appropriate and constructive. There is no need to be rude. Be respectful and considerate of the writer's feelings.

· Be sure that your comments are clear and text-specific so that your peer will know what you are referring to (for example, terms such as "unclear" or "vague" are too general to be helpful).

· As a reader, raise questions that cross your mind, points that may have not occurred to your peer author.

· Reread your comments before passing them on to your peer. Make sure all your comments make sense and are easy to follow.

Adapted from:

Pedagogy in Action [Internet]. 2019. SERC; [August 2019; August 2019]. Available from: https://serc.carleton.edu/sp/library/peerreview/tips.html

Rebuttal to Reviewers and Editor

· Your rebuttal letter and final versions are due in the D2L dropbox by the beginning of class on week 5.

· A rubric for this assignment is available.

Peer-review is a hallmark of good science. It is performed when we want to publish a scientific paper or write a grant proposal. In essence, other scientists review the work and give feedback/suggestions about things that should be corrected, are difficult to understand, language that is inaccurate or misleading, alternative interpretations for experimental results, etc.

Once the reviews are received, examine which suggestion are appropriate to take and which you do not want to change. As the author of the work, you do have the prerogative to ignore the suggested edits. However, if you do it is customary to defend your reasoning in the form of a rebuttal letter that is sent back to the editor with the revised work. The rebuttal letter should include all changes made, all suggestions not made and reasoning for why they were not made.

Note: Your responses must be respectful. Abusive language is unacceptable and will be heavily penalized. (In the real world, calling the reviewer/editor an idiot will get your paper rejected!)

- Formatting: Format your rebuttal as a letter to the editor (your instructor). It is customary to thank the reviewers for their comments before you describe what actions you took to change (or not change) your review. Your rebuttal should be 1 to 3 pages in length (including the description of changes).

- Description of changes: You will receive 2 reviews for your sections. Respond to reviewer 1 and 2 in separate sections of the same letter. Describe how you have responded to the reviewer’s comments. If you have opted not to make changes requested by a reviewer, you must fully justify why you’ve not made that change.

An example of a real rebuttal letter with description of changes, etc can be found on the D2L page.

Peer review guidance for Introductions.

No matter what area you pursue in your career, at some point you will have to give feedback to peers, those you supervise, or your bosses. Providing helpful critique is an important skill. You should be honest, helpful and direct. You should not be cruel or abusive, nor vague and uncritical.

This will be done on the discussion boards

Review 3 peers’ introductions, give them substantive suggestions on: - do the ideas follow in a logical fashion? - is the writing clear? -do the sentences make sense>? - are the ideas connected and relevant to each other? - is the grammar correct? (and spelling!) The author should have done a grammar and spell check before submitting, so don’t spend too much time on this area.

Note: -mouse gene names are formatted with only the first letter capitalized, and the name in italics: Olf554 -mouse protein symbols are the same, but not italicized: Olf554 -human gene names are all capitalized, and italics: OLF554 -human protein symbols are all caps, no italics OLF554 (the full name, olfactory receptor 554 is just usual text)

- species names should be italicized: Mus musculus or Homo sapiens

In text references with the CSE format are expected. The format is: last name of the first author, comma year in parentheses. If there are only two authors, provide both names, more than 2, use first name and et al.

Specific questions:

Does the writing introduce the reader to the broader topic and include interesting and relevant facts?

Is the writing clear, organized well and flow well from one idea to another?

Is the text grammatically correct with no spelling errors?

Are in text references in the correct format?

Is the literature cited section included and in the correct format?

Are images (if used, not required) appropriate and helpful to communicate an important concept?

What are the general strengths of introduction?

What are the general weakness?