Category Archives: General

Deconstructing the Written Comprehensive Exam

We've all felt like this at some point leading up to comprehensive exams. Photo from Flickr user Jixar, used under CC license.

We’ve all felt like this at some point leading up to comprehensive exams. Photo from Flickr user Jixar, used under CC license.

This article appeared in its original form at Gradhacker.org on March 22, 2013.

The dreaded written comprehensive exam. Many graduate students will have to pass some form of comprehensive exam at some point in their program. This can often include putting together a multi-page grant-style project proposal. Putting one of these together for the first time can be a daunting process if you are unprepared. But have no fear, there are ways to make crafting a solid document far less painful and even somewhat enjoyable.

Now at this point I have to mention that this advice will be most relevant for students preparing an exam on their own projects in the style of an NIH grant. However, this basic approach can apply to putting together any large proposal for your project.

Write down your outline: This will be the skeleton of your whole document. What are the absolute key points that you want to address? In the case of a grant style document, pick out your three aims first so that they address your three highest priorities. Once you get your main points set, start fleshing out your sub-aims in order of the most important questions in each aim. It’s a good idea to get the outline set before you begin writing since it becomes more difficult to rearrange material effectively once it is written long-form.

Find the gaps in your subject knowledge: Now that you’ve got your outline it’s time to find the holes in your knowledge of the topic. Do as much as much of a literature review as you have time for. Start early if you can because it has been observed that prolonged contact with material leads to better learning than cramming at the last minute and will help you in dealing with the finer points of your material later on.

There is a limit to how much of a review is helpful for you, though. At a certain point too many citations will bog you down and will no longer add to your proposal; so make sure to use citations judiciously.

Write a full first draft as fast as you can: It doesn’t have to be pretty at first, you just need something to edit. The easiest way I’ve found to write these is to sit down with a copy of your outline and start writing down your ideas as they sound in your head, no matter how far that is from formal language*.  This can help find remaining gaps in the proposal which become visible as you get full ideas on paper.

(*I approached my own exam this way and the first draft of my proposal was HORRIBLE, but it did give me something to edit and helped me find the areas that I needed to fill in with further literature review. Now, at least 10 drafts later, I have something that I will be proud to turn in today. It was much easier having a rough document early on in the process to work with than trying to put it all together at the very end. )

Leave it alone:  Now that you’ve spent this much time thinking about, reading about, and writing out this draft you’re probably somewhat sick of it, to say the least (I know I was). This is the perfect time to put it away for a day or two. Go do something else that you enjoy and will take your mind off of the work. This serves two purposes: it helps you maintain your sanity by taking some time off to recharge, and helps you come back to edit the draft with a fresh perspective.

Keep editing and writing separate: Now that you have a first draft it may be tempting to edit and write in significant changes at the same time. Be careful with this, as you may get trapped in a loop where you’re spending too much time editing new material as you write instead of getting the new ideas fully on paper. Reserve your first read through to editing only and observe any remaining gaps that you have in the proposal.  After the first full read through and any additional literature review it’s time to write in new edits.

While straightforward and fairly simple, it can be helpful to have guidelines in mind while writing something as large as a comprehensive exam proposal. This can help take some of the dread out of the process so that you can enjoy the opportunity to put your own ideas together. As graduate students, a good deal of our work involves writing and communicating our ideas clearly

If you have the time, I also highly recommend reading “The Science of Scientific Writing” by George D. Gopen and Judith A. Swan. This is an extremely helpful article that focuses on how readers will read your document and tips on how to make scientific writing more understandable for a wide variety of audiences.

Do you have any advice for the written comprehensive exam? Please share it in the comments section below.

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Filed under General, Gradhacker Posts, Graduate School, Literature Review

Ask a Microbiologist #3: What’s in the almond milk?

Today’s installment of Ask a Microbiologist comes from a reader wondering what might be in that old almond milk in the fridge:

English: Raw Almond Milk

Raw Almond Milk (Photo credit: Wikipedia)

“I found an open container of almond milk in my fridge the other day and it was OLD – I’m talking it had been opened for at least a month at this point. I know that as soon as it’s opened, the pasteurized almond milk is immediately primed for bacterial breeding. I was just curious as to which pathogenic (entero) bacteria are most likely to colonize at this point; I’m curious because there were zero indications of growth (ie no swelling of the container and no abnormal smells, colors, or textures).”

-Wondering what’s in there

Well WWIT, I’m glad you asked this, as I was starting to wonder about my soy milk as well.

This is a very open ended question and three main ways to inoculate your drink that could potentially lead to different contaminating microbes, some of which could be pathogenic. Continue reading

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Beyond Fever: Fungal infections and the benefits of body heat

Histopathologic features of aspergillosis incl...

Histopathologic features of aspergillosis including the presence of conidial heads PHIL 4335 lores (Photo credit: Wikipedia)

So far on this site I’ve tried to address microbiology topics from all areas of the field; from the standards in bacteriology and virology to some more exotic parasites and fungal infections. When you look at the range of infections that people can acquire you see many bacteria, viruses, and parasites. However, invasive fungal infections, especially those that occur in healthy immune-competent hosts, are exceedingly rare when you compare mammals to insects, plans, and amphibians. I never gave this much thought until coming across a group of papers that together indicate that something as fundamental as a warm body temperature could protect us from a variety of pathogenic fungi.

Read on to see how endothermy may be a protective mechanism against fungal disease. Continue reading

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Filed under Fungal Disease, General, Mycology

Our genome is not ours alone

Dendrogram of various classes of endogenous re...

Dendrogram of various classes of endogenous retroviruses (Photo credit: Wikipedia)

The last twenty years have been marked by a veritable explosion in sequencing technology. The Human Genome Project and it’s completion in 2003 was the crowning jewel of this burgeoning genomics revolution and played a major role in my early introduction to science. I distinctly remember being a sophomore in high school completely fascinated with the fact that we as a species have taken it upon ourselves to read the basic text that makes us all human. It still awes me that we are capable of this level of technology and that it just keeps getting better, smaller, and faster. Case in point: I am currently sitting 20 feet from an Illumina MySeq, an object the size of a 1990s-era desktop computer capable of delivering sequencing results in 24 hours. The amount of information to come from this branch of science is literally mind-boggling and only grows with each passing day.

Interesting observations have come out of this massive amount of genomic data relating to the  non-coding DNA in our genome. Less than 2% of the over 3 billion nucleotides in our genome are responsible for coding all of the protein that makes up a human being. This leaves a large question as to what exactly that other 98% of our genome is up to. Large parts (roughly 50%) are known as “junk DNA” with no accepted role, although new research is beginning to shed light on the functions of this DNA. The remainder of our genome is composed of long and short repeated sequences, transposons, retrotransposons and the topic of today’s article: endogenous retroviruses.

These elements are not human, they are fully viral in origin. This means that our genome is not just ours alone, we carry the DNA of many viruses that infected our ancestors in every cell in our own bodies.

Keep reading to find out what an endogenous retrovirus is, why exactly these viruses have invaded our own genetic code, and the implications of this discovery for the treatment of modern retroviruses such as HIV… Continue reading

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Passion for Communication

microphone

microphone (Photo credit: TOM81115)

Today I’ve been thinking about all of the influences that have made me so passionate about scientific literacy and effective science communication. As a global society we are challenged daily with obstacles that can most effectively be solved using our modern scientific understanding of the world. Yet for a variety of reasons much of the general public is unaware of the startling leaps and bounds generated by the modern global scientific community, aware but misinformed by sloppy reporting, to downright distrustful of science and those involved.  While we could go into these various issues and their origins at length, I would rather take a moment and share some of the resources that have pushed me to share my love of science with the public in the hopes that I can spread my passion for scientific communication to others. Continue reading

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