Please read 3 peer-reviewed papers pertaining to your project (obviously these

Please read 3 peer-reviewed papers pertaining to your project
(obviously these must not be the same 3 as Lit. Review 1), and submit
1.5-2 pages discussing the papers and their relationship to one another.
Background papers that help you understand your project topic are also
OK. The structure is flexible, but you could for example write one
paragraph about each and then relate them in two or three longer
paragraphs. Review papers and original research articles are both fine.
Google Scholar is a great resource for finding these. You are of course
allowed to include more than 3 papers if it would benefit the passage
you want to write, but make sure you’ve read three in depth.
The goal of this
assignment is to practice writing about papers in relationship to one
another. Generally when you read scientific introductions, you won’t
see the authors just summarize a single paper. Instead, they’ll talk
about how sets of papers relate to one another and to the topic at hand.
This turns out to be way more fun and creative than just summarizing a
single paper, since there are many different ways to think about how a
set of papers relates to one another and to a particular topic.
This is an
individual assignment, but it’s totally OK to discuss tricky
figures/methods in your papers with other folks in your group and the
broader class. Each group member should find their own 3 papers to
review.
Some examples:
— Read three papers about software tools/algorithms that do the same
task (e.g. the MUSCLE, MAFFT, and CLUSTAL papers), and compare and
contrast their approaches, accuracy (if they did benchmarking), etc.
— Read a theoretical paper that makes predictions, a software paper
that implements them, and a results paper that applies the software to
real data.
— Read three theoretical papers and consider what data/analyses/experiments would distinguish their predictions.
— Read three research papers asking similar question, and try to
work out what results they agree on (that may represent a general
trend). Where they disagree, is there a clear reason for the
disagreement? What types of data or experiments do you think could
resolve it?
— For a multi-step process like phylogenetic inference, genome
sequencing, or microbial community analysis, read a paper (or papers)
pertaining to each step.
A few hints:
HINT 1: one goal of the assignment is to strengthen the background
and discussion sections of your project. So it’s totally OK and
encouraged to write this in the format of the introduction or discussion
of a scientific paper, and then integrate all of your teams literature
syntheses into your Project 1 or Project 2 papers as appropriate.
HINT 2: For technical or methodological papers, the Supplementary
Information often has a much clearer description of the methods than the
main text.
HINT 3: You can cite papers in the middle of your text using the (authorname year) convention. For example,
“BLAST (Altschul 1990) is a commonly used local alignment search algorithm”
HINT 4: It can be helpful to skim many abstracts to get a sense of
the types of papers out there on a topic before settling on which you
want to read in detail.
HINT 5: If you find one good paper, the references in its
introduction and discussion may suggest additional papers to check out.
Important addendum on academic honesty and synthesis :
It goes without saying that to meet academic standards you must first read and take notes on the articles, then think about their content (leave time to do this). Then
based on your thoughts, write about the article. Finally, it is OK to
cross-check your writing with facts in the article after you have
written it. What you must not do (which you no doubt already know) is to
transcribe from papers and then modify the transcript. That’s
plagiarism, obviously, even if you modify extensively. A single instance
of it gets folks thrown out of academic labs or graduate programs,
fired from jobs etc (I’ve personally seen this happen, and it sucks).
More to the point, it’s boring and produces writing with lots
of buzzwords that makes literally no sense. The person it ultimately
disrespects most is the writer themselves. I am much more interested in your ideas, how you think about the material and connect it to other things you know, where you see
opportunities, etc. It is far better to write a paper that isn’t great
but reflects where you are with the material than to try to
short-circuit the process. Often bad writing is a key step on the path
to doing work which is great. If you are really thinking for yourself
about the material carefully, your writing will progress quickly with a
little revision.
Please use this 3 articles:
https://www.mdpi.com/2073-4425/11/7/761/htm
https://www.sciencedirect.com/science/article/pii/S0888754320320000
https://academic.oup.com/bib/article/23/1/bbab382/6369601