How to write a scientific paper, in four simple steps

Accomplished scientific writers will all have their own tips on how to go about writing a scientific paper. However, when you are first getting started, sometimes it is easier to have a set of steps available. Certainly there are many options available, but I personally have been finding the following set of steps useful when advising students lately.

• Step 1: Write the Introduction (starting with second paragraph)
  The introduction lays out why you bothered to do the study you did. It provides a background from the existing literature, and it points out holes in that literature or opportunities to test answers to questions that have little coverage.
  
  However, the first paragraph of your introduction (in fact, the first few sentences of your paper) are often the hardest ones to write. A colleague points out to her students that a great way to get around this potential writer's block is to simply skip the first paragraph. If you start with the second paragraph, you can immediately start laying out the argument for why your study needs to be done. Once you finish the rest of the introduction, it may be easy to see what the first paragraph needs to be. In other words, once you have 75% of the argument completed, the shape of the puzzle piece that remains will often be clear.
  
• Step 2: Write the Discussion
  If someone is already convinced that your paper has something interesting to say, that person will likely jump straight to the discussion and start reading there. This is where you describe how your data support some story that you want to tell about an inference you have made about the natural world. As you write your discussion, it will become clear exactly which data you need to tell your story. And so that brings us to the next step.
  
• Step 3: Write the Results
  Now that you have crafted a convincing discussion, you know what results are needed to support your argument. Writing the discussion first tells you what to include and what you can exclude. A lot of students make the mistake of starting with all of the possible plots that can be generated and then trying to string together a discussion around them, even if some of those plots really aren't needed. Don't do it that way. Instead, let your discussion guide which results to include.
  
• Step 4: Write the Methods
  Putting this step here is controversial. In many cases where your study has a clear experimental design that tests for something very specific, then it is possible to write your methods first. However, if you are instead working with a very large dataset that might someday result in multiple papers, then your methods might need to wait for you to determine exactly which results you need to make your argument. So once you've written your results, you can then generate methods that explain how all of those results came about.

Those four steps can often soothe writer's block on a scientific paper. You may determine a different flow as you mature in your writing process, but this is just one suggestion of where you might think about starting.

Special Note: Title and Abstract

Of course, two things that are left out of the steps above are the title and abstract. Young writer's often leave these until the end, and they often view them as complementary to the rest of the article. However, with maturity, it should be possible to write them first and view them almost as alternatives (or marketing pieces) for the whole article. Writing them first can also provide structure (similar to an outline) for the rest of the article. So work toward being able to write these two things first, but it's OK if you start by writing them last.

Keep in mind that most readers will only read the title and abstract (and some will only read the title). Consequently, the title should not be clickbait; the title should be an executive summary of the article, giving the punchline as opposed to begging the reader to read further. Interested readers will move on to the abstract. Consequently, your abstract should really have everything an educated reader needs to reconstruct your article; it should have a little bit of all of the sections. Your abstract should concisely say why you did the things you did, how you did them, what the main results were, and why those results are interesting.

Take-away Message: It's About the Reader

People are busy, and they allocate their reading resources accordingly. If you tease them with half statements, they will only get frustrated and move on to the next thing that competes for their time. Instead, give them something interesting and complete in the title. If they want more details, they can read the abstract, which should itself be complete. If they want more details, they'll read the main body (possibly starting with the discussion section). For the reader, it's about sequentially choosing what to read next. When you write, you should always have this in mind as you design the delivery vehicle for the content you hope will be disseminated broadly.

"Dark Matter is an Illusion" summary in National Geographic News gets something a little wrong

There was an interesting article from National Geographic News yesterday:

"Dark Matter Is an Illusion, New Antigravity Theory Says"
by Ker Than

I thought I'd post a link to the primary source here. I also wanted to point out that the explanation Ker Than gave got something really important wrong and consequently diminished the elegance of the proposed theory.

Here's the primary source:

"Is dark matter an illusion created by the gravitational polarization of the quantum vacuum?"
by Dragan Slavkov Hajdukovic
Astrophysics and Space Science 334(2):215--218
DOI: 10.1007/s10509-011-0744-4

Ker Than, the National Geographic News reporter, got it a little mixed up in this part of the NatGeo article:

All of these electric dipoles are randomly oriented—like countless compass needles pointing every which way. But if the dipoles form in the presence of an existing electric field, they immediately align along the same direction as the field.

According to quantum field theory, this sudden snapping to order of electric dipoles, called polarization, generates a secondary electric field that combines with and strengthens the first field.

This electric analogy states that electric dipoles align and strengthen electric fields, but that's incorrect. Electric dipoles weaken surrounding electric fields. In particular, the positive end of the dipole goes toward the "negative end" of the field and the negative end of the dipole goes toward the "positive end" of the field. So the two fields subtract from each other, not reinforce. This is summarized in the primary source (that I'll quote below).

[ note that magnetic dipoles align and reinforce surrounding magnetic fields because there are no magnetic monopoles. That is, magnetic field lines are continuous; they don't terminate. Consequently, magnetic dipoles are torqued to align their fields. Electric dipoles are driven by the motion of their monopolar ends ]

What Ker Than missed was that in this model of "gravitational charge", it is the case that opposites repel and likes attract. That's why you (matter) are attracted to earth (also matter). However, anti-matter and matter would repel each other. Moreover, if you had a matter–antimatter virtual pair (as quantum field theory says you do in a vacuum of space), that dipole would align because its "positive" end would be pulled toward the positive end of the gravitational field (and vice versa for its negative end). This alignment would strengthen the resulting field.

Here's the relevant snippet from the bottom of the first column of page 2 of the article:

In order to grasp the key difference between the polarization by an electric field and the eventual polarization by a gravitational field, let's remember that, as a consequence of polarization, the strength of an electric field is reduced in a dielectric. For instance, when a slab of dielectric is inserted into a parallel plate capacitor, the electric field between plates is reduced. The reduction is due to the fact that the electric charges of opposite sign attract each other. If, instead of attraction, there was repulsion between charges of opposite sign, the electric field inside a dielectric would be augmented. But, according to our hypothesis, there is such repulsion between gravitational charges of different sign.

Breathing is carbon neutral, asshole

It's not uncommon to hear people say things like, "Carbon neutral? What's that? Wouldn't you have to stop breathing? <huh huh> <huh huh>"

The carbon in the carbon dioxide that you exhale is a product of cellular respiration inside your cells. It comes from breaking down sugar (a carbohydrate). The process liberates the carbon from the sugar so that it can bond with the oxygen that you inhale to form carbon dioxide and water (e.g., urine or "pee"), and this releases energy since carbon would much rather be a part of carbon dioxide than sugar. This energy is what you use to go about your day and say statements like the above.

So where does the sugar come from? It what is produced in the photosynthesis that goes on in plants. Photosynthesis uses energy from the sun to reshuffle water and carbon dioxide into oxygen and sugar.

That's right. The carbon you exhale comes from sugar that could not have been made without pulling carbon out of the air.

So that's why breathing is carbon neutral.

This is also why combustion, which is related to cellular respiration, of pure biofuels (hydrocarbons) is POTENTIALLY carbon neutral (see notes about sustainable yeilds); the carbon in those fuels was originally pulled out of the air by a plant somewhere, and hopefully more plants will pull it out of the air after combustion. Of course, there are lots of other things involved in combustion (e.g., processing and transporation of biofuels as well as the consumption that goes on in the process of burning those fuels) that are not carbon neutral (and, again, there's that issue of burning so many plants that you don't have any left to take the carbon out of the air; again, see sustainable yield).

You should consider these things when you think about livestock as well. Breathing does not prevent something from being carbon neutral.

So what isn't carbon neutral? If you are releasing carbon that did not (recently) come from a plant source, you are probably not being carbon neutral. Burning fossil fuels is liberating carbon that has been buried for (hundreds of) millions of years. This is why the word fossil is used. This carbon would have stayed buried if it was not for human intervention. This causes a stability problem on the surface of the earth. The carbon cycle gets out of whack because that extra carbon does not go back to its source. In fact, the only way to get that carbon back to where it came from is to have a mass extinction and then millions of years of geological processes.

So that's the scoop on carbon neutrality.

Do (Reuters) reporters know absolutely nothing about everything?

UPDATE: It was pointed out to me by a post on Nanotechnology Today that the Professor who heads up the research group that built the "demon" said (speaking about J. C. Maxwell):

"As he predicted, the machine does need energy and in our experiment it is powered by light. While light has previously been used to energise tiny particles directly, this is the first time that a system has been devised to trap molecules as they move in a certain direction under their natural motion. Once the molecules are trapped they cannot escape."

Again, what's going on at Reuters?! This quote is EXACTLY the opposite of their summary (quoted below).

It's just silly that the article "1867 nanomachine now reality" has gone the extra mile to be completely worthless. It's also silly that CNN has decided to put this in their "Offbeat news."

The experiment described in the article involves Maxwell's Demon, which is a thought experiment involving a "paradox" of statistical thermodynamics. However, nowhere in the article is this paradox ever mentioned. In fact, they go so far as to say this:

His mechanism traps molecular-sized particles as they move. As Maxwell had predicted long ago, it does not need energy because it is powered by light.

Now, I'm guessing that the scientists involved said that Maxwell's paradox was a paradox because his little demon did not require additional energy. However, this device doesn't cause any paradox because their demon DOES require additional energy IN THE FORM OF LIGHT. As I explain to my fourth graders, light is energy. Nearly all of the things that end in "cycle" in the study of earth and life science are driven by the energy brought from the sun in the form of light.

Anyway, the article completely misses the point and is filled with lots of misunderstandings and statements which could generously be called wrong.

Do they have editors at Reuters? To cut costs did they just fire them all and hire the cast of Who's the Boss? instead?