Many out there may know that I have a nice lofty title at PLoS Biology. I am the Academic Editor in Chief there. With this title I get a lot of complaints about PLoS Biology.
Alas, despite my lofty title, I do not actually run PLoS Biology. You see, PLoS Biology is a hybrid journal with both Professional editors and Academic Editors. The way it actually works is that the Professional Editors, under the direction of Theo Bloom, run the journal. As part of their running of the journal, they consult with Academic Editors (AEs) to get help in deciding if papers should be reviewed; if they are reviewed the AEs help suggest reviewers; and once reviews are back the AEs help in making decisions about the fate of the papers. They also consult AEs about a variety of other topics.
In the end, you could view the AEs, including the AEIC (that is, me) – as having an advisory role at PLoS Biology. Generally, decisions are made in a collaborative manner with the AEs but in the end, it is the professionals who make the “final” decisions regarding the journal. But they do listen when I tell them about what the community likes and dislikes about PLoS Biology.
Anyway, the reason I am writing is that in two weeks there is a meeting in San Francisco of the EICs of the various PLoS Journals and I will be going to this meeting. So here is my request:
I WANT YOUR COMMENTS ABOUT PLOS BIOLOGY.
What do you like?
What do you not like?
What new things would you like to see?
What would you like to get rid of?
Please either post your comments here, on twitter, or friendfeed or wherever. Or send them to me by email. And I will try to communicate them to the powers that be …
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Jonathan Eisen's Lab 
I enjoy science book reviews — I know PLoS Biology has maybe one per month, but Science and Nature have several per week. There may be a good reason for limiting them in PLoS Biology, though — I don't know if they hurt the impact factor based on the way ISI calculates it or something.
Also, I enjoy the news relating to science that are in Science and Nature. It would be great if PLoS Biology had something similar, but maybe that would be impractical without a paid reporting staff.
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Book reviews are one of my favourite parts of any journal.
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It seems to me that it is a step backwards to have another non-peer-edited journal. The idea that the “professional” editors are in charge rather than the academic editors is not conducive to improving the science that is published. Thus, I encourage you and the other academic editors to foment a revolution and take control as soon as possible. I realize that the professional editors are presumably often making decisions that improve the immediate rating or impact factor of the journal. The academic editors, though, would presumably be sometimes making contrary decisions that, although reducing the journal's short-term visibility factory, would improve it's scientific integrity and long-term academic reputation.
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The review process is glacially slow.
Supplementary material is expected to be convertable to PDF format, which is exactly wrong. Supplementary material should be for electronic files that are unsuited for inclusion in the PDF paper (either because of size or format). “Supplementary material” in PDF either belongs in the paper itself, or doesn't belong.
And I second David Pollock's comment.
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Re: PDFs in supplemental material – that definitely has to change
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And I third Sean's second of David's comment.
Jonathan, I think you know my views on this subject, which I explicated in Genetics, Feb 2009; 181: 355 – 356.
I _sincerely_ believe that peer-editing is AT LEAST as important for a healthy scientific enterprise as is open access.
Mark Johnston
EiC, GENETICS (the peer-edited journal of the Genetics Society of America)
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Mark
I was sadly unaware of your editorial. Here is a link to it for those interested. It is titled “Reclaiming Responsibility for Setting Standards” and is certainly worth a read … methinks I might be sending it around to a few folks …
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You could start publishing the anonymous reviews alongside the published papers, as we do now at all journals published by EMBO (see example [PDF]).
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completely agree thomas – I think reviews and reviewer names should be open
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