How Not To Write A Scientific Manuscript

Friend of the DoucheMonkey blog Sol Rivlin had the following to say in response to other friend of the blog Isis the Scientist’s query to her minions regarding how to handle unexpected or unplanned experimental outcomes when writing them up for publication:

As to the unexpected results. My suggestion for you is to be truthful about your intial intent and expectations and to tell the story as it happened, including the unexpected. In reality, that is exactly what happens to many of us, but too frequently, we are tempted to appear smarter than we really are, pretending that the unexpected outcome was actually very expected and that we knew exactly what will happened long before we did the experiments. Most scientists tend to lie in this way, we know they lie because we have done it ourselves and yet, we continue doing it.

That ranks among the absolute stupidest gibbering dumbfuck advice concerning manuscript preparation I have ever seen or heard.

No one reading scientific literature qua scientific literature gives a flying fuck about the internal mental state of a scientist when she performs an experiment. All anyone cares about in this context is the conceptual relationship between the novel information revealed by the experiment and the existing conceptual landscape. Period.
The mental state of scientists when they perform experiments may be of great interest in other contexts, for example to sociologists or philosophers or to their mothers or something like that. But for scientists operating in a particular scientific arena reading the scientific literature in that arena, the internal state of the scientists performing experiments is nothing but a distraction from what they really want and need to know.
And the idea that it is “lying” to say, “In order to test the hypothesis that blah induces bleh, we generated a transgenic whoozis expressing fuckdribble in the bleezer”, when what really happened was you thought, “I wonder what the fuck would happen if we expressed fuckdribble in the bleezer”, represents as pathetically deficient an understanding of how scientific discourse works as it is possible to have.
Every single fucking scientist ever born knows that most experiments are performed to see what the fuck would happen if you performed some particular manipulation on some particular thing. And every scientist knows that “In order to…, we did…” is a *fiction*. But it is an exceedingly convenient and useful fiction, because it makes it much easier for the reader of a scientific paper to embed everything she is reading into the appropriate conceptual framework as she reads along.
Building suspense is for shitty novels and hackfuck horror movies. No scientist wants to read, “We decided to see what the fuck would happen if we expressed fuckdribble in the bleezer, and MUCH TO OUR SURPRISE WE FOUND (DRUM ROLL, PLEASE)…HOLY FUCKNOLY!! WOULD YOU BELIEVE IT? THE BLEH WENT KABLOOIE! So, then we scratched our asses and drank some Jameson down at the motherfucking bar, and realized that, HOLY FUCKNOLY!! THIS RESULT TESTS THE HYPOTHESIS THAT BLAH INDUCES BLEH!”
It’s a waste of the intended readers’ time and mental effort to write scientific papers that way. How many times do you need to read, “In order to see what would happen, we…” to get the point? Employing a convenient and useful fiction that everyone understands to be a fiction, but that everyone agrees to be both convenient and useful is not “lying”.
And as long as we’re talking about this kind of “lying”, let’s address the issue of the order in which experiments were performed versus the order in which they are presented in a paper. By Sol’s definition, virtually all scientists are “lying” when they write their papers, because the experiments were almost never performed in the order in which they are presented.
Authors might even use phraseology like, “Having established that the flanknozzle is hikerny (see Figure 1), we then flinked the flanknozzle”, when they know damn fucking well that they flinked the flanknozzle months before establishing that the flanknozzle is hikerny. LIARS!!!!!!111111!!1!!11!!1!!!!
Again, this is a convenient and useful fiction that everyone knows is invariably employed. You present results in the order that makes sense conceptually in order to make your readers’ life easier.
For example, when scientists try out a new experimental manipulation, they frequently employ it first in the very complex experimental context that they actually care about in order to see if it is going to yield interesting fruit. If it does, then they go back and fill in various experiments performed in simpler, more reduced, contexts to provide convincing evidence that the new manipulation does, indeed, do what it purports to.
But from the standpoint of the reader, it makes their lives much easier if they are first presented with convincing evidence in simpler contexts that a novel experimental manipulation is effective at doing what it purports to, before then describing the novel insights into some biological question that is has revealed in a more complex, yet interesting, experimental context. This is called “crafting a convincing story”, and everyone knows, expects, and desires that the authors of the scientific papers they read do so.