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Suppose I disagree with the methods and/or conclusions of a paper published in a scientific journal, and I produce some new results that refute the claims in this paper. What would be the best way to publish my contradictory results in a way that challenges the original paper, but also shows respect for the authors of the previous paper? Should I explicitly mention the positive merits of that paper before explaining why I think that the conclusions are wrong? Or would it be implicitly assumed that I disagree only with the previous paper's scientific conclusions, and I have no negative feelings towards its author(s)?

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    In my opinion, in academia, what you say or write about someone's research (directly or indirectly) should always represent only your arguments about scientific merits of the research, but never your "feelings" toward authors (regardless of how right or wrong those feelings might be). As far as politeness goes, it is implied in academia and beyond, as an essential element of professionalism and work culture/ethics. – Aleksandr Blekh Oct 23 '15 at 5:18
  • If you write a paper that is very much focused on that other paper (like a "Comment on ..." type), I've often seen people introducing early in their comment paper an abbreviation for the first paper. Say you are critiqueing a paper by Smith and Jones (2012), then you would write e.g. "the SJ12 paper is wrong about ..." which sounds much more polite than "Smith and Jones (2012) are wrong about ...". – semi-extrinsic Oct 23 '15 at 8:54
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    "Wrong" is a fairly heavy statement to make, and one that I would avoid (especially if it turns out to be an incorrect statement). For politeness, I would say that it is best to place yourself on the same level as the other party rather than take an authoritative stance. – Jake Oct 23 '15 at 9:20
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I would like to ask a counter question; what it the main motivation in you wanting to publish your contradicting results and your disagreement with the authors of that one paper?

I think the main motivation of a publication should be to add something to the literature, not the discuss results back and forth. That's what conferences are for.

Without knowing the specifics of your particular case at hand I see the following possibilities:

Experiment presented is not the best way to test the hypothesis

If your reasons for refuting the article originates from the approach presented in the paper, then you are merely proposing an alternative approach to solve the same problem.

That's the easiest scenario, in my humble opinion, since you can easily refer to Smith et al. and say that your approach is superior/more accurate compared to theirs because X,Y,Z. That would essentially be a standard "original research" paper.

Incorrect results

if you have tried to replicate the experiment by Smith et al. and cannot come up with the same results, then you can adopt the following steps in that order:

  1. Redoing your experiment, once more, retracing your steps to make sure you have done exactly as explained by the authors.

  2. Contacting the authors to tell them that you cannot replicate their results and whether or not there might be a key step that you might have overlooked. This is a sign of good faith for your fellow researchers.

  3. In the case where despite all your efforts there is something just not right, you can try contacting the editor with evidence on contradicting results, which may lead to a correspondence type paper. This approach might come across as a more or less accusatory approach however.

Misleading conclusions of results

If you think the specifics of the experiment (or equivalent) are solid but the conclusions drawn and presented are misleading, you can write an opinion piece, or a commentary and send it to the editor.

Be sure that the discussion (i.e. whose conclusions is more accurate) is actually relevant to the general audience in that field. Otherwise it's just scientific banter which can be carried out by email.

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Should I explicitly mention the positive merits of that paper before explaining why I think that the conclusions are wrong?

Yes.

What does it hurt to say something nice? The key is to find something meaningful to be nice about.

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    Specifically, when you write your related work and describe the contributions that the paper made over the previous work, you'll be saying something nice. But then when you contextualize what you are doing relative to what they did (i.e., your contributions), you will make it clear what was the oversight in the other paper. – user38309 Oct 23 '15 at 6:45
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Firstly, research isn't a contest and the authors of your mentioned paper are certainly not your rivals. Have you considered contacting them? Refuting their work directly, without doing so, may appear slightly rude.

Secondly, "stating your opinions" about their research at most belongs in a footnote, certainly not in the main body. If you want readers to believe the original method was incorrect, try to convince the reader in the most transparent way possible: science. If your method is better, prove it. If you can explain why their method wasn't as good, just contrast the two.

"Our method is based upon that of R. McDonald's 2014 paper{cite}, but we opt to use Thermite instead of flour; we base this decision on research by D. Evil, showing that Thermite has been shown to be more fun than flour in the bread-making process{cite}."

Whether or not you cite the research explicitly in the text depends on the journal's style guide. If it uses numbering, a direct mentioning of the author's research in the text body (as opposed to "just" a citation) is as polite as you can get.

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When describing papers in general, when your results conflict with the one in another paper. You may do the following.

  1. State the positive outcomes of the paper (that is not in contradiction)
  2. State the matter that contradicts with your belief and how so.
  3. Show how your results defend your belief.

Note that your aim is to defend your theory and not to attack the previously stated one.

It is natural for theories to evolve as further research goes on. We all know that the atom was first proposed to be an indivisible element which was then later found out to be composed of protons, neutrons, and electrons. Then, muons and mesons were discovered. In nowhere along these lines did the author of the successor had to worry about opposing the theory of the predecessor. That is the beauty of science.

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