The document provides guidance for students on drafting an introduction and hypothesis for a biology writing assignment. It includes tips for brainstorming topics, incorporating relevant scientific facts, leading into a specific research question, and ending with a clear hypothesis statement. Students are instructed to write an initial 1-page draft, submit it for peer review, and then provide a rebuttal letter addressing peer feedback along with a revised draft. The document emphasizes avoiding plagiarism and properly citing sources.

1. 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.

2. 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

3. 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/cae
norhabditis_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

4. 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

5. 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

6. 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

7. 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.

8. 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

9. 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

10. 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?
The first citation I got was from PubMed and citations 2-5 I got
it from PubMed Central.
References

11. Ren M, Qin H, Kitamura E, Cowell JK. Dysregulated signaling
pathways in the development of CNTRL-FGFR1-induced
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Jun 13].
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3739028/
T; GTLHUG. 99m Tc-Hydroxydiphosphonate Quantification of
Extracellular Matrix Mineralization in 3D Human Mesenchymal
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Chakrabarti S, Pattison LA, Singhal K, Hockley JRF, Callejo G,
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TRPV1-dependent manner. Neuropharmacology. 2018 Dec
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277850/
JK; RMQHKEC. Dysregulated Signaling Pathways in the
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Pouzo LB;Descalzo AM;Zaritzky NE;Rossetti L;Pavan E;
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