Debbie Knight

That’s the report I’m filing: the scientific manuscript

In observation on January 16, 2013 at 9:30 am


A friend of mine, a fourth-year graduate student, just submitted a manuscript to the scientific journal PLOS One.

Her name is listed as the first author on this, her first manuscript submission.

It’s a pretty big deal to write that first first-author manuscript. It’s your research, it’s your baby.

Naturally, she’s very excited about it.

It reminded me of my first first-author manuscript, written so many years ago. I remember it was quite a task to write the beast. It consumed a large part of my life while I gathered and graphed data, plunged into the existing scientific literature.

The writing did not come easily for me.

Every word was written knowing full well that it would be heavily scrutinized by my boss, the reviewers and other scientists.

By the time the manuscript was submitted to a scientific journal for review, my boss had so heavily edited what I wrote I barely recognized it as “mine.” I was really surprised my name was still first.

It was a humbling experience.

But it was a huge learning opportunity.

My next manuscript was a little easier to write.  And a little more of my writing remained untouched.

When that first manuscript was accepted and published in a scientific journal, I sent copies to everyone I knew. It was so cool to see my name in print, to have my research efforts out there in the scientific community.

It’ll be interesting to see how my friend handles it if and when her manuscript is finally published.

Of course the manuscript will have to run the gauntlet of editors and scientific reviewers.

Best case scenario is the manuscript is accepted for publication with no changes required.

But more likely, the reviewers will have some issues that she will have to address either in writing or through more experiments. In this case, she would need to make the necessary changes and resubmit the manuscript for further scrutiny.

Then there’s the worst case scenario. The journal’s editors will reject the manuscript because the work is not appropriate for their journal. In this case, she would have to take stock and retool the manuscript to submit to another perhaps more appropriate scientific journal.

I have my fingers crossed for the best case scenario!


So what does a scientific manuscript look like?

It is pretty much a technical report. It has a very defined structure, a formula if you will.

First is the introduction which puts the research in context – historically as well as biologically. The last paragraph of the introduction should include what your data shows.

This isn’t storytelling where you hold the punch line until the end. Everything is revealed up front.

I find the introduction one of the hardest things to write.

Quite a bit of digging through the scientific literature happens before the first word is written. And including the appropriate depth of literature review is tricky.

The next section in most scientific manuscripts is the material and methods section.

This is where I usually start the manuscript writing process.

I advise any first-timer to start here!

Why? It is by far the easiest part of the manuscript to write. It involves writing about what reagents you used and how you performed the experiments.

If you kept a very meticulous lab notebook, all this information is at your fingertips. Reagent specifics such as catalog numbers, supplier names and company addresses as well as antibody clone designations, antibody isotypes and associated molecular tags are often needed in this section. Sometimes that means you have to hunt for the data sheets that came with the reagent or dig through a stack of packing slips to find the specific details you need for this section.

You learn quickly to include this information in your lab notebook after you’ve worked on your first manuscript.

The next section is the results section. This is the next easiest section to write — although it’s not nearly as easy or straightforward as the materials and methods section.

This is where you tell your research “story.”

Here you present the data as graphs, tables, figures, photos, etc.. Each figure needs a description, a figure legend, that should be able to stand alone. Sometimes this is the only thing a reader will read in the article.

Generally, the first line of the figure legend summarizes what the figure is showing – kind of a title or a headline.

It is then followed by a brief description of the method used as well as what the figure shows.

If written well, the reader shouldn’t need to even look at the accompanying image.

What’s tricky with the results section is figuring out what data presented in what order will help you tell your story best.

Many researchers tell the story how it unfolded, often starting with the original observation that sent them on their journey.

The researcher will then show how they proved what they thought was happening was actually happening.

Sometimes that story takes a twist – an unexpected outcome of their investigation. I find these most interesting to read, to see how researchers roll with the punches.

Sometimes the story unfolds in a straightforward and logical manner.

Sometimes the researcher offers their interpretation of the data in this section, but more often the significance of their discovery is discussed in the last section, the hardest section to write, the conclusions (or sometimes discussion) section. In this section, the researcher places his data in context with other scientific data. This may require a lengthy explanation why his data flies in the face of other scientist’s data.

Some researchers expound on the subtleties of their findings.

Some researchers will wax philosophical. Some will stand on their soapbox.

There is quite a bit of style variation in the conclusions section.

And, yes, there is a bit of overlap in these various sections.

You need the overlap because different readers start at different places within the research article. Some readers will only look at the conclusions. Some are only interested in a particular method or a particular part of the puzzle.

I know that I can read the same paper at different points in my research project and get very different information out of that paper. At the start of the research project I might only be interested in a particular method. At another stage of the project, I might want to see what their data looked like or how they interpreted their findings.

So there you have it. Scientists do their research, perform the experiments to better understand a phenomenon, and report their findings to the scientific community. (At least that’s how it happens in the university setting.)


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