Following up on the earlier discussions of intentional unclarity and bad writing in scientific papers, I thought this might be a good opportunity to consider an oft-cited article on scientific papers, P.B. Medawar's "Is the Scientific Paper Fraudulent?"  He answers that question in the affirmative only three paragraphs in:
The scientific paper in its orthodox form does embody a totally mistaken conception, even a travesty, of the nature of scientific thought.
Medawar's major complaint has to do with the "orthodox form" and the story it tells about how scientific knowledge is produced. The ordering of major sections in the sort of scientific paper he decries is pretty recognizable in much peer-reviewed scientific literature today:
- Previous work
As far as they go, Medawar seems tolerant of the introduction (which places the scientific question addressed by the paper in a larger context), the run down of previous work on the question, and the description of the methods used in collecting and analyzing data. But he views the last two sections as problematic:
The section called "results" consists of a stream of factual information in which it is considered extremely bad form to discuss the significance of the results you are getting. You have to pretend that your mind is, so to speak, a virgin receptacle, an empty vessel, for information which floods into it from the external world for no reason which you yourself have revealed. You reserve all appraisal of the scientific evidence until the "discussion" section, and in the discussion you adopt the ludicrous pretense of asking yourself if the information you have collected actually means anything.
These two sections, he suggests, have scientists pretending to have engaged in a process quite different from the one actually involved in their research.
One of Medawar's big complaints against the standardly formatted scientific paper is that the story it tells reinforces a picture of scientific inquiry that Carl Hempel describes  at the narrow inductivist view. According to this picture of science, scientists start out by observing and recording all the facts about the world. Next, they analyze and classify these facts. Then, they use induction to derive generalizations - claims like "all ravens are black" or "the gravitational force between two bodies is proportional to the product of their masses over the square of their distance." Finally, they subject these generalizations to further tests.
This is an appealing view. Science sticks to the facts. It looks at how the world is and pulls out the patterns that connect the individual facts, getting the evidence first and building the theory from that. But, according to Hempel, science couldn't work this way.
For one thing, we never have all the facts. There are many bits of the world as yet unobserved, and the future is not something we can experience at all until it becomes the present (at which point there is still, we hope, a whole lot of future stretching ahead). Whenever we're trying to derive generalizations from partial information, we have to face the problem of induction.
But there are other problems with this picture of science. Even if we're only going to collect some of the data, which data should we collect? Hempel says that scientists rely on working hypotheses to guide their decisions about which observations to pay attention to and how to classify their data. Rather than reading their hypotheses off the world, scientists start out with hypotheses in order to get good observations of the world.
One more issue here is that Hempel says that induction is not an automatic process for generating generalizations from your stack of data. Rather, "the transition from data to theory requires creative imagination." If lots of data are missing, it requires insight to make a good bet about what it all adds up to, or about what's going to happen next.
As a philosopher of science, Hempel had ample opportunity to notice that narrow inductivism couldn't be a good description of how science really works. However, Medawar notes that the way scientific papers describe the scientific inquiry seems to be maintaining the fiction that this is really how scientist operate (or at least, how they should operate; otherwise, why tell the story that way?):
What is wrong with the traditional form of the scientific paper is simply this: that all scientific work of an experimental or exploratory character starts with some expectation about the outcome of the inquiry. This expectation one starts with, this hypothesis one formulates, provides the initiative and incentive for the inquiry and governs its actual form. It is in the light of this expectation that some observations are held relevant and others not; that some methods are chosen, others discarded; that some experiments are done rather than others. It is only in the light of this prior expectation that the activities the scientist reports in his scientific papers really have any meaning at all.
Medawar (and Hempel, too) finds Popper's picture of scientific activity more plausible. Popper saw two quite distinct parts of the scientific activity, the generation of hypotheses and the testing of hypotheses. Hypothesis testing is all about working out what your hypotheses logically entail and then setting up observations or experiments to compare what you ought to see if the hypothesis is true with what you actually see. The testing part of the scientific activity, as far as Popper is concerned, is nicely grounded in deductive logic (dodging the problem of induction). Besides conducting careful experiments and making good observations, all you need to do is feed in hypotheses that are falsifiable and you're good to go.
Where do these falsifiable hypotheses come from? Popper doesn't think it matters. Maybe they're hunches you develop while slaving in the lab or poring over the literature, but they could just as easily be ideas that come to you at cocktail parties or in fevered hallucinations. As long as they're falsifiable -- and as long as you are setting out making your best effort to falsify them -- they'll provide the necessary input to the glorious deductive testing machine of science.
This Popperian picture, whatever you think of it, is in stark contrast to the narrow inductivist picture in which scientists "feign no hypotheses" but simply collect the data and read the patterns off the world -- the picture of science Medawar thinks most scientific papers convey.
Why should this "fictionalization" of the process of scientific inquiry matter? In part, it misrepresents science to the public -- making it out to be more cut and dried, objective, mechanical, and boring than it really is. As well, it may be indicative of a way scientists mislead themselves -- thinking they have to achieve the super-human ability to read the correct generalizations off a pile of (necessary incomplete) data, or that good scientists never depend on luck or inspiration. Indeed, this latter issue may be the one that's really bugging Medawar:
The scientific paper is a fraud in the sense that it does give a totally misleading narrative of the processes of thought that go into the making of scientific discoveries. The inductive format of the scientific paper should be discarded. The discussion which in the traditional scientific paper goes last should surely come at the beginning. The scientific facts and scientific acts should follow the discussion, and scientists should not be ashamed to admit, as many of them apparently are ashamed to admit, that hypotheses appear in their minds along uncharted by-ways of thought; that they are imaginative and inspirational in character; that they are indeed adventures of the mind.
Why should scientists pine for an ideal of scientific inquiry that is both unattainable and that, were it somehow attainable, would make them boring cogs in a machine rather than the adventurers of mind that they really are? Why not be honest -- and proud -- of the human element of how science is really done, and report it that way?
Would anyone like to respond to Medawar on this?
 P. B. Medawar, "Is the Scientific Paper Fradulent?" Saturday Review, 1 August 1964, 42-43.
 Carl G. Hempel, Philosophy of Natural Science Englewood Cliffs, NJ : Prentice Hall, 1966.