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Hey-hey-hoo, science nerds and fellow H. sapiens!

Heheh. I had to go geek here.

Not science papers!

As a result of some trouble in one of my courses this semester, I have put on my TA cap and have typed up how I read a scientific paper.  Its nitty gritty, stepwise and colloquial.  Exactly the opposite of a scientific paper.  But hopefully, it will give you a bit of a better insight on what you shouldbe looking for when it comes time to sit down and read it.  Its much better than having it in one eye and out the other. So, without further adieu, lets delve into it!

  • Step 1: The Title.  Why yes, you should start with the title, where else?  The title is going to tell you exactly, in no uncertain terms, what it is you’re going to be attempting to plug through in the next few pages.  Wait, but oh no, big words!  If you encounter a word you don’t know or an organism  you’re not familiar with, google it.  Why?  Because although the internet’s information should never be trusted for stringent details, it can give you the overall gist of what it means or what it is.  Also, pictures can be a boon here.
  • Step 2: The Abstract.  What is this bold paragraph that sits directly beneath the authors’ names?  The abstract is a concise, to the point paragraph that gives you (in general terms): 1) what they did. 2) what happened 3) a small summary of why they think its important.  This is another great way to check to be sure you’re going to at least understand what the heck is going to be said in this paper.  Don’t skip these two.  Knowing ahead of time what you’re going to be reading is an important part of reading scientific literature.  This isn’t like reading your novel of choice and not reading the end because it would spoil it for you.  Trust me, you want to know what the authors are going to say.  We, as scientists, must critically analyze what is being said, not just believe it.  Knowing what they think beforehand allows us to process what they are saying in the meat of the paper and compare it to what they asserted in the title and abstract.

Just to give you a recap of what we’ve done so far, my thought process once I’ve read both the title and the abstract should be: “Okay, the title said kryptonite turns on randomgeneX which causes atomic powers in mice and the abstract says they think kryptonite activates randomgeneX by…  It is important because…”  What I am saying here is after you’ve read the title and abstract, check to be sure you know what is being studied, what the basic result was and its purpose.  If you can’t quite figure it out, google the words and ideas you don’t know.  If you can, excellent, lets move on!

  • Step 3: The Introduction.  Now, the introduction is solely in the paper to give the reader background knowledge on randomgeneX that activates mouse atomic powers when upregulated by kryptonite.  The authors know that only a small percentage of the scientific community have had any sort of experience with atomic mouse powers and therefore provide background information; leading their readers in a small history lesson.  This information should bring you some semblance of an idea of where the authors started and got their hypothesis from.  Science, like all literature, is built upon the lessons and works of others.  Just like every author cites inspiration and every idea is never truly novel, each experiment in science has some basis in past research and discoveries.  Sure, there are a few “avant-garde” experiments here and there, but it is hardly ever the case that someone’s work is not built upon a foundation of those who came before them.  Once you’ve read, and googled if need be, the introduction, you should be able to answer why the authors did their research in the first place.
  • Step 4: The Materials and Methods. Reading the M&M can be a daunting task for anyone, especially those who have not been in or around a wet lab.  However, you all may sigh in relief because all I ever do in my first pass through a paper is skim the techniques.  Why?  Truly, because all you need to know is a general idea of what was done.  In more modern papers, kits (like from Invitrogen) are often sourced for their methods and if need be, their websites contain detailed information of how things are done.  But for our purposes, we just need the bare bones.  Read the M&M to find gene names, clone names, what techniques were done and any other information that might be beneficial to the rest of the read.  Don’t try to get every detail down, its not worth it at this point.
  • Step 5: The Results.  Alright, here we are.  The bulkiest and most important part of the paper.  How on earth do we tackle this?!?  Easily and stepwise.  Unlike in a textbook where you can look at figures ahead of time to get an idea of the things you will be reading about, the figures in a scientific paper are often best not looked at until they are needed.  Scientists are notorious (in my experience) for writing bad figure legends and captions.  So, instead, start reading.  Take it slow, take each point they are trying to make bit by bit.  Stop after every major point (usually each paragraph) and summarize it to yourself.  Did what they just say make sense, considering the background information?  When you reach a citation for a figure, stop and look at the figure.  Use the first few sentences of the image caption to orient yourself and find out what is being displayed.  Is it a blot?  A gel?  A phylogenetic tree?   Here is the point where, if need be, go back to the M&M and familiarize yourself with the technique if you do not understand it.  Now that you know what the figure is, think of what you expect it to tell you. Then, look at the image, given what you know, and ask “Does this make sense with what the authors’ said?”.  Usually, it is yes.  If you’re still not clear, read it again, look at it again; step yourself through what the figure is supposed to tell you.
His weakness is cheese.

His weakness is cheese.

Lets stop here and do an thought game.  Say that the authors of the atomic mouse paper show an agarose gel in which a reverse transcriptase-PCR was performed with primers targeting the mRNA of the randomgeneX in two conditions: kryptonite+ and kryptonite-.  Before we even think about the author’s exertion of kryptonite causing expression of randomgeneX, think about what the agarose gel should show us.  An agarose gel stained with EtBr would show bands of DNA that have been amplified by the PCR.  We would expect to see no bands in the lane in which the kryptonite- was run, while the lane with kryptonite+ should have a band at whatever size randomgeneX is.  Then, we examine the figure itself and find, lo and behold, that yes, there is a bright band in the + lane, but none in the -.  Therefore, the authors are right in asserting that randomgeneX is transcribed when kryptonite is present.

Once you’ve done this for all points made in the results, go back and summarize it for yourself.  Get a good idea of what exactly was done–what were the exact results?  Knowing these things will help you critically analyze the authors’ opinions in the next section.

  • Step 6: The Discussion.  It is in this section that our authors attempt to correlate what they’ve learned in their study to other research done in a similar fashion.  They will make points about the importance of their discovery in relation to other systems/organisms/fields.  It is up to you, who now knows what the authors know, to look at what they say and see if you agree.  Remember the introduction, as the information stored there often plays a role in the discussion.  Ask yourself, given what you know about the study, what conclusions you would make and would they match the authors’.
  • Step 7: Wrapping It Up. Once you feel you’ve got a good idea of the paper, tie it all together as a whole picture in your mind.  Write yourself your own abstract, detailing briefly what the meat of the paper was all about, as well as its implications for the field of science as a whole.  Bullet points are excellent for this.
Post-paper understanding...

Post-paper understanding...

I hope that this guide will help you begin to understand how to address scientific papers.  They are a tough bunch to read and must be approached differently than any other type of written work.  Remember that these papers are a presentation of evidence as a defense for an “idea” in which the authors have about atomic mouse powers and their regulatory systems, to use our running example.  Once you begin to examine them as something to be critiqued and analyzed, rather than something to be read and understood, scientific papers become almost second nature to read.

Best of luck and happy reading!

The Alchemist Kitten

Hey hey hoo!

All, I am working on a bit of a biographical post for you all.  But, while you wait ever so patiently on bated breath, my darling readers, here’s a bit of a co-op I did with a friend!

Retrogaming 101–Legend of Zelda: Ocarina of Time

I really like to play older video games and this is the first of a few that we will be co-authoring.  GASP! No, no, my life does not consist wholly of science and study.  In fact, I’ve done nothing this summer but read, drink and play WoW. So, enjoy another bit of my awesome life, readers.  And give Cluttered Mind a bit of your patronage!