Dr. Mom, My Adventures as a Mommy-Scientist

Discussion of my journey from grad school to postdoc to tenure with two kids, a husband, (and a bit of breast cancer) in tow.

Thursday, October 20, 2005

Writing your first paper: Step Five: Materials and Methods

Thanks for all your supportive comments about my post yesterday. I'm really not depressed or anything, but sometimes my frustration just builds and builds until you get well...the post from yesterday. Anyway its time to move on with my series on writing papers.

This article is part of a series on writing your first research paper. I am hoping to use this material for a new student handbook when I start my faculty position, so any thoughts, comments, hysterical rejoinders are most welcome.

Note: All data is made up, but you can make ice cream with liquid nitrogen.

Materials and Methods

This section is so straightforward that I was tempted not to write about it. However, there are a few things that I would like to point out so here goes.

If you are unsure where to start your paper. This is it. It is the easiest section to write because their is no interpretation. This section should describe your experiments, as you did them, in enough detail for someone else to repeat them. There should be absolutely no discussion of results here.

The materials and methods section will not be read by most people. The people who do read it are doing so because they want to repeat a portion of your work, or perform similar work. They will therefore want as many details as possible.

The materials and methods section is usually broken into sections, with one section for each experimental component or reagent/equipment preparation. Each section should contain the following elements:

For reagents: List the catalog number, manufacturer, and their location.

For equipment: List the settings, model number, manufacturer, and their location

For experimental solutions: Describe how the solution was made using exact numbers. In many cases it is better to describe a liquid solution in molarity so that it may be scaled to any volume by a reader. If multiple concentrations were used then add a table to describe the conditions examined.

For an experimental set-up/apparatus: Describe all the components used (including equipment information above) and how they are connected. If necessary, draw a diagram. This is especially helpful for complex organic synthesis, manipulating biological pathways, or when constructing complicated reactors. However, it is rare to see photos of the actual apparatus, as a schematic is much more instructive to the reader.

In the materials and methods section, language is very important. The kinds of phrases you might use in an internal lab protocol would not be appropriate here. For example, "don't heat that up too high or it will turn black and come crashing out of solution!" becomes "heat to 95 degrees C, taking care to monitor temperature closely. Excessive heating may result in product decomposition and precipitation." Professionalism is important here, and in many cases, little things are left out. If the reader requires more detail, he/she can always email the authors directly. You might find, "add eggs to warmed milk solution (50 degrees C), while stirring" but not "add eggs to warmed milk, taking care not to scald, stir counterclockwise, then clockwise, use some of milk solution to rinse egg container, then stir continuously."

There is a fine line in how much detail is provided. Some authors leave out things on purpose, to retain their lab's ability to manufacture the product in question to the exclusion of others. This is not very professional (unless of course you are applying for a patent and have IP issues). Science is based on the ability of hypotheses to be tested by individual investigators. If you withhold information, expect others to become angry and frustrated with your papers, especially if they cannot reproduce your results. If IP issues really are a concern, it is appropriate to say "using a proprietary compound" or "please email for more information."

However, if there is a safety hazard, it is important to describe it in as much detail as possible to alert the reader. Don't say, "be really careful, it might blow up," but do say, "heating to temperatures in excess of 100 degrees C will likely result in catastrophic explosion."

Below is an example section for ice cream preparation using liquid nitrogen:

Creating Ice Cream with Liquid Nitrogen

Ice cream was prepared using liquid nitrogen (LN2) as a freezing medium [99%, Air Products, Hopkington, MA]. Liquid nitrogen can cause burns and thermal stress. Use proper PPE (e.g., cryogloves) and do not use ceramic materials, which may crack, in preparation. To create LN2 ice cream, The ice cream mixture was placed in an oversized (10X final target volume) steel bowl. Liquid nitrogen was added slowly (~ 1 ml/s) in a single stream in a 5:1 ratio to the ice cream mixture while stirring. Freezing was monitored visually, and using a Fisherbrand cup-type viscometer [Fisher Scientific, No.: 1; Orifice Diameter: 0.078 in.]. Ice cream was determined to have formed when viscosity change fell to less than 5% min and visual thickening was evident.

The title and first sentence describe what this section of the Mats and Meths will cover. Note that the purity, company, and location are listed for the LN2. If someone cannot repeat my experiment and is worried that differences in reagents may be the cause, they can obtain exact duplicates using this information. Seems trite, but in many experiments reagent source can be very important! [Something to keep in mind if ever your experiments are hit with an endless stream of failures.]

The safety concerns come next. Some people like to put these later in the text, but I am always worried that someone may not read all the way through and it is better to put this stuff up front. Safety concerns to the body and to equipment are both listed. It does no good to have someone carefully using gloves and lab coat only to have the container crack, spilling LN2 everywhere. To avoid liability it is always better to say, "use proper PPE." This places the burden on the reader to determine what they think constitutes proper PPE. If you know that certain things are required it is okay to say, "use proper PPE, including cryogloves" or like I did "(e.g., cryogloves)." I cannot emphasize how important it is to outline experiment safety; you do not want to be responsible, even indirectly, for another's injury!

The next few sentences describe the preparation of the ice cream from the ice cream mixture. [The mixture was presumably described in the preceding section.] I used general terms (e.g., 10X bowl, 5:1 ratio) to allow the reader to scale the reaction to his/her system. Note that the speed of addition is important and was therefore given. If not sure what the exact number is, it is okay to estimate.

Finally, I discussed how we determined that the reaction was complete. Of course we can just look at it (e.g., visually), but we also use the more scientific technique of measuring viscosity. We need some way to know when reaction is complete, so I said when viscosity changed less than X % over X time, but in combination with visual observation. It is possible that viscosity doesn't change because reaction never took place, so it is important to combine these two observations to determine that ice cream has been made.

This pattern continues for each section needed in the mats and meths.

7 Comments:

At 6:07 AM , Blogger Kim said...

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At 5:44 PM , Blogger Google Page Rank 6 said...

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At 10:14 PM , Blogger Kim said...

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At 2:47 AM , Blogger Antonio Hicks said...

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At 6:35 AM , Blogger Daniel said...

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At 6:54 PM , Anonymous Anonymous said...

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At 6:38 AM , Blogger Freddy Meyers said...

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