Monday, January 26, 2015

How to Write a Scientific Paper

As I enter the latter stages of my PhD, I'm working to summarize all the stuff I've done over these past four and a half years in a series of publications that will ultimately become my thesis. This sounds daunting and tedious, and it most certainly is...but not for the reasons you would think. Here is a guide for all you first-time paper writers out there!


Beginning to write the paper can go one of two ways:

1) you want to publish your work because you feel that you have finally gathered enough data to make an important contribution to the scientific literature
2) your advisor comes to you saying we need to publish this paper RIGHT NOW or your sworn enemy lab will scoop you

Gather your data. Discover that you didn't write down the one piece of relevant information that you need in your lab notebook. Panic, then try to rationalize how you can write the paper without that one critical piece of information.


Frantically write the paper

Wait three months while the paper sits on your advisor's desk

Try to find your advisor. Discover that he has left the country for a month without telling anyone.

While you are waiting, perform an experiment that you think will support your paper's conclusions and add to the breadth of data. Experiment contradicts your previous results, and you need to change the entire paper.

Re-write paper in a frenzy and send out revised version

Wait again, as your advisor has gone to a conference for the week.


Receive edits from your advisor. Re-write the entire paper for a third time. 

More Edits.


Co-author who hasn't said anything up to this point suddenly decides that everything is wrong in the paper and it needs to be rewritten. Re-write the paper for a fourth time.


Endnote library crashes.

You decide to accept all of your advisor's edits because you are now nauseated by looking at this paper and don't care anymore. Time to submit! 


Almost there!

Attempt to fit your text into an excessively complicated Word template that was last published in Word 2003. Discover that Word 2003 and Word 2013 really don't like each other. Don't even get me started on Mac/PC compatibility.

Even though you already included your figures in their template, the journal requires that you upload every figure and table individually. Your image size will exceed the file size required for figures. Sucks. You're getting JPEGs, jerks.



This never happens just by itself. If your paper is simply "Accepted", there has likely been an error. 

Accepted with major revisions or Accepted with minor revisions

Major and minor are clearly in the eye of the beholder. Either category can range from redoing figure captions to redoing the experiments that the entire paper was based on.

Reviewer #3 will think your paper is terrible no matter what. Get out your thesaurus and figure out the most tactful way to say "You are an idiot" without insulting the editor.


Try submitting to our sister journal that no one has ever heard of! Impact factor: 0.5


Appeal the decision. Fight! Fight! Fight! This may or may not be successful, so proceed with caution. 

Congratulations! You have successfully written a scientific paper! Elapsed time: 18 months

Sunday, January 18, 2015

Crockpot Mulled Wine

Okay, so technically, the holiday season is over, and all things spiced and fragrant are considered passe. However, it is freezing here in Chicago, which means to me that warm drink season is still in full swing.

I love to make crockpot mulled wine for dinner parties because you can just throw all the ingredients into the slow cooker and forget about it while you are busy preparing everything else. The longer you cook it, the better it gets, so it is basically a foolproof recipe!

This mulled wine is also a very economical way to entertain for a crowd because you can use the cheapest wine you can find, and it will still taste amazing. I used some Three Buck Chuck from Trader Joe's. Just make sure you have a dry red wine, and you're set!

The wine was so popular that I didn't even get a chance to take a picture of it, so you'll have to trust me when I say that it looks very impressive and welcoming!

Crockpot Mulled Wine

Science & Cupcakes Original

Makes approximately 20 servings

3 750 mL bottles of dry red wine (I used Charles Shaw's finest Cabernet Sauvignon)
1 large navel orange, cut into quarters
16-18 whole cloves
4 pieces star anise
6 cinnamon sticks (about 3 or 4 inches long)
1/2 cup brandy
1/4 cup honey
1/4 cup brown sugar, packed
1/4 cup orange juice

Using a knife, make small holes in the peel of the orange. Stick the cloves into the holes. This technique makes it easier to keep track of all of the cloves so that you don't have to fish them out of the wine later.

Add all ingredients to a large crockpot. Cover and cook on high for 4 hours or until ready to serve, stirring occasionally until the honey and brown sugar are dissolved. Drink and be merry.

Tip: If you have cheesecloth, you can also make a little sachet with all of the spices in it. I didn't have this, but it still worked out fine!

Sunday, January 4, 2015

I'm back!

Hello, friends!

It has been entirely too long since I've posted. This past quarter has been CRAZY. Between TAing, lab work, writing papers, etc., I've barely had any time for myself. However, the best thing to happen over the past few months was this:

(Photo credit: Adrienne Matz Photography)

Andy and I are married! We couldn't have asked for a better day. Everything went smoothly, and everyone seemed to have a great time, as is summed up in this picture.

(Photo credit: Adrienne Matz Photography)

I promise that I have lots of recipes coming up in future posts in addition to more grad school wisdom as I get closer to thesis super funtime (!) in the next months. Ahhh! Thanks for sticking with me during my lengthy absence, faithful S&C readers! Love you all.