Can I revise a part of the paper that the reviewer did not mention?

Question

I received a major revision recently. However, as I was making revisions, I realized that my first draft from a few months ago is badly organized and poorly written.

I want to make some changes to a part that the reviews did not complain about.

My advisor told me to only focus on the question raised by the reviews. And reminded me that making unrequested changes is very dangerous and can even bring up rejection. His point was that the parts of the manuscript that the reviewers did not raise questions about proved to have been satisfactory and accepted.

I personally agree with my mentor in general. However, without changing the original purpose, I hope to improve the quality of the article by better writing and expression, or even new experiments. Is it acceptable?

Answer 1

I realized that my first draft from a few months ago is badly organized and poorly written.

I think there is a fine line to be drawn here. Based only on your description, I do not think that this is the appropriate time to reorganize your paper, as your advisor said, parts of the manuscript that the reviewers did not raise questions about proved to have been satisfactory and accepted. If they did not ask you to reorganize your paper, then receiving a reorganized paper to review again might be frustrating.

Working on your phrasing in individual paragraphs is better, but again, you are asking the reviewers to reread the entire paper, and giving them a much bigger list of changes to work through. I think your advisor is overstating the risk of rejection (but I don't know the reviewers in your field).

However, without changing the original purpose, I hope to improve the quality of the article by better writing and expression, or even new experiments. Is it acceptable?

New experiments is a very different question, and a domain-specific one only your advisor can answer. You can (should?) perform new experiments to address specific problems the reviewers raised, but performing them only to enhance your paper at this stage raises an eyebrow.

In short, I would feel free to wordsmith as appropriate, but otherwise follow your advisor's advice carefully.

Answer 2

You can do this (but doing it well requires experience)

If you were an experienced researcher, rather than a PhD student, I would say that you should certainly revise in the way you think makes the paper better. Since the paper has not yet been accepted, you are free to revise it in any way you think will improve it. This includes making revisions that have not been suggested by the referees. If you make your paper better somehow, they are unlikely to object, and at worst this might just require some more revisions in the next round of review. I have made unrequested changes to papers a few time after receiving referee reports (just because I concurrently thought of an idea to make it better) and in all those cases the paper has still been accepted.

The only real issue here is that you are a novice researcher, so you probably do not yet have good judgment on what makes a paper better/worse. (And the fact that you now think your previous draft was badly organised and poorly written also suggests this.) Therefore, there is a danger that your proposed revisions might either make things worse, or at least move things around unecessarily without making things better. If this were to occur then the referees might indeed be a bit chagrined, and it could reduce the likelihood of acceptance.

Fortunately, you have at your disposal a supervisor who is probably pretty good at determining better/worse on these matters. In view of this, I recommend you write up a new draft with your proposed revisions and seek feedback from your supervisor on whether your (unrequested) changes have unambiguously improved the paper. If you think you have a good idea to improve your paper, have a go at this. Your supervisor should then be able to give you some guidance that is conditional on seeing the actual revisions you have made.

Answer 3

Yes, it is legal. The paper is yours until you give up copyright to it.

I think your advisor may be worried about the consequences if reviewers don't think your changes are actually improvements. Or worse, make the paper less publishable.

But since you were already asked for major changes I think the risk is small if you do a bigger revision. It might, probably will, slow the next review process, but if it does result in improvements that is better for everyone.

Adding new experiments, however, might best be saved for a follow-up paper. Changing the scope of the paper, in general, is likely to result in delays (at best).