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Open Access Highly Accessed Open Badges Editorial

A community experiment with fully open and published peer review

Eugene V Koonin*, Laura F Landweber and David J Lipman

Biology Direct 2006, 1:1  doi:10.1186/1745-6150-1-1

PubMed Commons is an experimental system of commenting on PubMed abstracts, introduced in October 2013. Comments are displayed on the abstract page, but during the initial closed pilot, only registered users can read or post comments. Any researcher who is listed as an author of an article indexed by PubMed is entitled to participate in the pilot. If you would like to participate and need an invitation, please email, giving the PubMed ID of an article on which you are an author. For more information, see the PubMed Commons FAQ.

The importance of revision

Gregory O'Kelly   (2006-07-04 12:19)  San Luis Neuroscience Laboratory email

The previous comment from Stephen Mount suggesting that once revisions were made to a submitted paper there was no reason to include the criticisms that led to these revisions, is, putting it mildly, naive in the sense that it implies that finished papers contained the information that was of key importance, and that all revisions are minor and peripheral. Science is a process, not a body of knowledge. Those who are interested in and familiar with the subject matter of an article, can still stand to benefit greatly from the response to criticisms by the author. In fact the treatment by the author of hypotheticals and exceptions which otherwise seem to test the rule, can be very instructive and either demonstrate the robustness of or highlight the infirmity of both theory and hypothesis. That this is not the standard method of the publication rat-race only goes to emphasize the uniqueness of this site, a uniqueness which, in earlier times, was commonplace and marked by communications between men of letters commenting upon each others work and telling of personal discoveries. This era started to come to a close during what I. Bernhard Cohen, in his REVOLUTION IN SCIENCE, termed the third scientific revolution, which was the way science is done. This closure began in the first part of the twentieth century, and was marked by intense specialization and institutionalization of research. Stephen Jay Gould, in an essay in BULLY FOR BRONTOSAURUS, describes this move as the end of garage inventors and experimenters who would change their fields dramatically. Men from Mars, he called them, people who would appear out of nowhere with accounts that challenged and advanced scientific knowledge, if they were listened to. Alfred Wegener was one of this sort. He is the one responsible for the theory of continental drift, reviled and ridiculed in the late 1920s and 30s. His ideas are now canonical.

It is exceedingly important for those watching that they see how a new hypothesis or theory is able to deal with or dismiss the factual schemes that are claimed to be arrayed against them. This gives the reader a better feel for the validity or the weakness and insignificance of new, alleged revelations. It is in the handling of objections and criticisms that new theoretical constructs are elucidated and refined,or discarded, and it would be a shame to deny the community sight of the author struggling to deal with these offerings. Might I recommend the essay "Falsificationism and the Methodology of Scientific Research Programmes" by Imre Lakatos in the book CRITICISM AND THE GROWTH OF KNOWLEDGE, for its treatment of the subject of why revision is important to the scientific process, regardless of what motivates it? It would be misleading to the new people to think that all ideas sprung fully formed into print. It is important to see how new schemes assimilate, explain, or dismiss old facts. Only in this way is the flexibility or rigidity of new explanations manifest.

Gregory O'Kelly

Competing interests

None declared


Differences between the submitted and published versions of papers

Stephen Mount   (2006-06-12 14:37)  University of Maryland, College Park email

Under the current system, reviews generally suggest changes that are addressed in a revised version. Many reviews are full of minor suggested revisions with which the author is happy to comply ("clarify the axes in Fig. 3," "consider citing Smith et al." and so on). It makes no sense to have these suggestions be part of a permanent record if they apply to a version that is different from what ultimately gets published. In some cases, the authors would probably prefer that no on know about problems they've fixed. In general, reviews address a version that differs from what gets published. How is this going to work?

Competing interests

None declared


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