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A paper describes a computational method for solving a problem, and we made a significant improvement to the method and applied it to a new case study. Is it appropriate to publish a response paper?

Most response papers I've seen dispute the findings or methods of the paper they are responding to. Is it reasonable to write a response paper which agrees with the initial paper?

EDIT: It wasn't very clear when I first posted this, but the "response paper" I refer to is a specific mechanism that journals have for responding to an existing paper published in their journal. This is often called a comment or discussion paper. At Nature, they're called "brief communications arising". I might be the only one that calls it a "response paper," actually...

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In general, 'comments' can be comments in support or comments in disagreement. Usually people tend to only submit comment when they are moved strongly to point out a disagreement.

But, as question specifically referred to Nature's "brief communication arising" (BRA) the answer is NO. The BRA notes that "Submissions should challenge the main conclusions of the Nature paper and contain new, unpublished data to support the arguments.". (i.e., pointing out errors, reinterpreting conclusions, coming to a different end result, comments to refute). Showing that there is an alternative method that is better than that presented in the paper doesn't seem to fall under that 'challenge' to the paper. (Unless perhaps you can write it as challenging some final conclusion that their method is the best possible ever? )

They offer the option to add extensive comments under the paper on the website. But then it will be difficult for others to be able to cite or even find your work. It sounds as if you should find a journal and submit your your method as improvement in XX algorithm/method, citing the original Nature paper.

For comments and criticism there is a brilliant new service of pre- and post-publication reviews called Publons. For example, a recent and very harsh criticism of a sensational paper in Nature. Each review is assigned a DOI, so others may easily cite your comments. Also, it is well covered with Altmetric, which provides quite a visibility to your comment. Yet, no official impact factor for you reply publication.

  • After reading a little more I realized that the "response paper" system that journals use is almost always structured as three publications: 1. Original article 2. Respondent's critical comment 3. Original author's response. So there would be very little point in the respondent agreeing with the original author because then the third publication would be something like this. – foobarbecue Apr 29 '16 at 2:57
  • The last paragraph is an addition to my answer. I might have not included the word 'brilliant' as a descriptor as it is not in mainstream use, (i.e. people like me (Carol) would likely be going the traditional 'comment' route mentioned earlier) but as a statement of fact, it is a new service. – Carol Oct 22 '16 at 14:16
  • Uh yeah, I'm pretty sure the edit system is not supposed to be used for expanding an answer like this, especially in this case where the new paragraph doesn't address my question directly. That's what comment system or Community Wiki is for. – foobarbecue Oct 22 '16 at 18:20
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Every paper, in some way, is a response to everything that it cites. You can respond in agreement as much as you can in disagreement. An improvement is a positive response and you might couch it more in terms of a follow-on or follow-up without having to be negative about the prior results.

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    I'm not asking about "every paper," I'm asking about a response paper. i.e. what Nature calls "brief communications arising" – foobarbecue Apr 28 '16 at 2:43
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    @foobarbecue, maybe you should add that to your question. I didn't know you meant something formal, so I gave an informal/philosophical response. – Bill Barth Apr 28 '16 at 2:55
  • Ok, added. extra characters. – foobarbecue Apr 29 '16 at 3:03
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To be direct,

Not always

A response paper with respect to an initial paper, X, can come under one or more of the following categories.

  1. A method that can outperform what is prescribed in X
  2. An improvement over the method implemented in X
  3. A conflict of results with that of X
  4. A different approach to the problem stated in X
  5. A sequel to X by providing additional information or different analysis

From the above, only 1, 3, and probably 2, applies so as to disagree with the initial paper, X.

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