The Manuscript Submission Process at Science (Magazine)

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Today Peter Stern, the Senior Editor of Science Magazine was here at the Genome Campus to give a talk about the manuscript submission process at Science. No matter where you are wr.t. scientific publication and the future of scholarly communication, the talk was very engaging, throughtfully delivered and mercifully done without any audivisual aids. I have made a few notes during the talk and here they are. They are unedited “live typing” and as such not pretty – but hopefully useful when trying to understand the publication process for Science. I have (mostly) refrained from commenting on what he said – though there could be a lot that could be said about this – but maybe at a later date. For now, just the raw unadulterated notes:

Peter Stern: The Manuscript Submission Process at Science
Three points to address:

1. Presubmission Enquiries
2. Board Members
3. Review Process

Ad One
Scientists sometimes forget the bigger picture as they work and get their results. Presubmission enquiries can be useful to get some feedback and help place work in some bigger picture. Insists on confidentiality of info provided pre sub enquiries.

Ad Two
Science has about 28 individuals trying to cover all of science….all editors have science profiles…multiple ones…many have run research groups.

Ad Three
Paper is submitted…Stern makes high play of safety and confidentiality. Paper gets assigned to editor. Editors try to read in full and form an informal opinion, but admits that this is getting harder due to volume of submissions. Now talks at great length about the “wackos” (creationists, people inventing perpetuum mobile). Editors work with advisors – “board members”….again about 10-12 advisors…..but they don’t do a review but rather try to place manuscript in the bigger picture of science. They come back with a short evaluation and a confidence score. Board members are active scientists with labs…..looks for gentleman factor in board members (wants to be sure that they are fair to papers even if paper disagrees scientifically with board member).

Once feedback from board members has been received editor opens another round of discussion with fellow editors. If there is a positive decision at this stage paper will be sent for full review. Most papers fail of this stage. Also little room for discussion – decision is essentially binary.

Finding referees: authors can prepare a “negative” list and a positive list of referees. Lists are usually respected…certainly the “negative” list. Editors often scan websites of grant giving bodies…to avoid friends/collaborators refereeing each other. Recommends “Guardians of Science” – a sociological study of the peer review process. Default options of two referees, sometimes more if necessary. Default review time of two weeks: seen as the right balance between speed an ensuring that authors din’t get scooped and allowing enough time for in depth review.

When referee comments come back, there is room for negotiation depending on comments. What happens next depends on what referees ask for. If it is reasonably further work, paper could go back to authors, if too much further work si requested editor has to make a decision. “Peer review is not a democratic process.” If referee reviews are all over the shop could use an arbitrator – which could be a board member.

If positive decision is made, editor will do a “pre-edit” to make it fit Science style. If author is native English speaker, editor will focus on logical argument and flow of paper, if non-native speaker, more linguistic help is needed. After pre-edit is done, paper is returned to authors and a revised version is expected back within 4 weeks unless experimental work needs to be done which takes longer. Most of the time revised paper goes back to referees and gets green light if referee comments have been addressed.

Once accepted papers can go onto science express for rapid publication and to allow the scientists to claim precedence of publication. This is followed by harsh copy-editing. Calls orthographic mistakes an “affront to science”. Now talks about how good they are at disseminating science and making their authors famous. Here’s the gatekeeper justification again.

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Data-Rich Publishing

I have been insanely busy recently with trips and papers and corrections and…etc…and only now have a bit of time to catch up with some of my feeds and people’s blog posts. One post which caught my eye was Egon’s recent blog post about data-rich or data-centric publishing, in which he argues strongly for a new kind of publishing: a publishing in which data is treated as a first class citizen and which allows/requires an author to not just publish the words of a paper, but his research data too and to publish it in such a way that the barrier to access by machines is low.

This reminded me of what I thought was a particularly tragic case, which I blogged about a while ago here. In this particular case, industrious researchers had synthesized an incredible 630 polystyrene copolymers and recorded their RAMAN spectra. Now this is more than a crying shame: a lot of work has gone into producing the polymers and recording the data. And I ask you (provided you are a materials scientist and have an interest in such things), when was the last time that YOU came across such a large and rich library of polymers together with their spectral data? And through no fault of their own, the only way these authors saw to publish their data was in the form of a pdf archive in the supplemental information.

Now Egon’s point was that newly formed journals – and in particular newly formed Journals of Chemoinformatics – have the opportunity to do something fundamentally good and wholesome: namely to change the way in which data publication is being accomplished and to give scientists BETTER tools to deal with and disseminate their data. This long and rambly blogpost is my way of violently agreeing with Egon: I believe that THIS is where an awful lot of the added value of the journal of the future will lie. This will be even more true, as successive generations of scientists will start to become more data savvy: last week I talked to a collaborator of ours who had just put in for some funding to train chemistry students in both chemistry and informatics: a whole dedicated course. Now once these students start their own scientific careers, they will both care and know about science and scientific data. And if I were a publisher, I would want to have something to offer them….

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Polymer Markup Language Paper

Now i started this blog with the intention of writing about polymers, informatics etc.. Somewhere along the way, some advocacy, some ranting and a general critique of the scholarly publication process also crept in and, of course, there were long breaks. However, we have recently published polymer markup language, which has been in the making for a while and I am pleased to announce the paper, published in the Journal of Chemical Information and Modeling:

Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language

Nico Adams, Jerry Winter, Peter Murray-Rust and Henry S. Rzepa

Polymers are among the most important classes of materials but are only inadequately supported by modern informatics. The paper discusses the reasons why polymer informatics is considerably more challenging than small molecule informatics and develops a vision for the computer-aided design of polymers, based on modern semantic web technologies. The paper then discusses the development of Polymer Markup Language (PML). PML is an extensible language, designed to support the (structural) representation of polymers and polymer-related information. PML closely interoperates with Chemical Markup Language (CML) and overcomes a number of the previously identified challenges.

Many thanks are due to everybody who worked on this and everybody in the Unilever Centre who was available for discussions, comments and critique.

The paper can be found here

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Copyright Permissions – How they can also be done!

Having recovered from my hopping madness vented in my last post by taking a brisk walk round the chemistry department, I sat down to request more re-use permissions. One of the figures I wanted to use came from PNAS – the Proceedings of the National Academy of Sciences. Their current copyright policy was explained in a PNAS editorial in 2004 (I quote the entire thing):

Liberalization of PNAS copyright policy: Noncommercial use freely allowed

Nicholas R. Cozzarelli, Editor-in-Chief, Kenneth R. Fulton, Publisher, and Diane M. Sullenberger, Executive Editor

We have changed our copyright and permissions policies to make it easier for authors and readers to use material published in PNAS for research or teaching. Our guiding principle is that, while PNAS retains copyright, anyone can make noncommercial use of work in PNAS without asking our permission, provided that the original source is cited. For commercial use (e.g., in books for sale or in corporate marketing materials), we approve requests on an individual basis and may ask for compensation. We have revised our copyright assignment form to make the changes clear ( and added to our web site a “frequently asked questions” (FAQ) section on author and reader rights (

As a PNAS author, you automatically have the right to do the following:

* Post a PDF of your article on your web site.
* Post a webcast containing material from your article.
* Make electronic or hard copies of articles for your personal use, including classroom use.
* Use, after publication, all or part of your article in a printed compilation of your work, such as collected writings or lecture notes.
* Include your article in your thesis or dissertation.
* Reuse your original figures or tables in your future works.
* Post a preprint of your article on a public electronic server, provided that you do not use the files created by PNAS.
* Present your paper at a meeting or conference, including those that are webcast, and give copies of your paper to meeting attendees before or after publication in PNAS. For interactions with the media prior to publication, see the PNAS policy on media coverage (
* Permit others to use your original figures or tables published in PNAS for noncommercial use (e.g., in a review article), provided that the source is cited. Third parties need not request permission to use figures and tables for such use.

Given that authors and readers can automatically use original material in PNAS for research or teaching, why do we request copyright transfer? We do so for three reasons: to allow us to publish, archive, and migrate articles to new media; to remove the administrative burden of rights and permissions management from authors; and to provide protection from copyright abuse.

We do not feel that this or any copyright policy is the only one possible. In fact, our policy has changed through our 90 years of publishing and surely will change again. We have requested that authors transfer copyright only since 1993. From the first issue of PNAS in 1915 through 1992, authors held copyright to their articles. From 1978 to 1992, we registered copyright for each journal issue as a collected work but did not request copyright for individual articles. In 1993, we began requiring that authors transfer copyright “in all forms, languages, and media now or hereafter known,” which granted us the rights to publish papers online in 1997 and to then digitize selected back issues and post them online.

We think that our current policy best meets the needs of readers, authors, and the journal, for the following reasons:

1. To store and migrate archival formats of the journal. We are committed to facilitating permanent, freely accessible archives of the scientific literature. PNAS is a charter member of PubMed Central, a digital archive of the life sciences journal literature (, and is a participant in the National Library of Medicine’s effort to digitize and post back issues of journals. Not holding copyright to individual articles from 1915 to 1992 delayed our posting of this older material online because we do not have the legal rights to do so. In the end we proceeded without explicit permission from the original authors or their heirs. We accept the risk in doing so because we believe it is clearly in everyone’s best interest. If a copyright holder objects, however, we will immediately remove the article from our online collection. Full copyright transfer allows publishers explicit rights to invest in long-term archiving strategies.
2. To provide an administrative convenience for everyone. Despite our liberal rights and permissions policies, PNAS still receives more than 50 commercial and noncommercial permission requests per week. We routinely agree to noncommercial use, so such requests waste everyone’s time.
Unfortunately, PNAS cannot provide permission for others to use all or part of articles published from 1915 to 1992 because we do not hold copyright. Only the original authors or their designees can grant permission. Researchers are frustrated when they contact us for permission to use seminal works and we are unable to grant their requests.
3. To provide international protection regarding infringement or plagiarism. On the rare occasion that material is misused, authors appeal to PNAS to intervene on their behalf to enforce copyright protection. In such cases, a formal query from PNAS or the threat of a copyright infringement lawsuit has prompted expeditious action. In cases of redundant publication we sanction authors for violating journal and copyright policy. Because international standards and copyright law are complex, PNAS leaves interpretation of global copyright standards to our expert legal counsel.

We also support creative efforts such as charting, mining, analyzing, sorting, navigating, and displaying information contained in PNAS. The highly successful Sackler Colloquium “Mapping Knowledge Domains” ( is a prime example (1). We encourage authors to use standard forms of data presentation to facilitate this process.


1. Shiffrin, R. M. & Börner, K., eds. (2004) Proc. Natl. Acad. Sci. USA 101, Suppl. 1, 5183–5310.[Free Full Text]

This is reaffirmed on the up-to-date 2007 PNAS copyright faq page:

Can others (nonauthor third parties) use my original figures or tables in their works without asking PNAS for permission?

Yes, PNAS automatically permits others to use your original figures or tables published in PNAS for noncommercial and educational use (i.e., in a review article, in a book that is not for sale), provided that the original source and copyright notice are cited. Commercial reuse of figures and tables (i.e., in promotional materials, in a textbook for sale) requires permission from PNAS.

Now this is an entirely sensible and science friendly policy. Now open access according to the BBB declaration, but a huge step in the right direction, certainly in comparison with the last example:

  • automatic grant of re-use rights for non-commercial puposes (because asking for permission and credit card numbers is a WASTE OF TIME)
  • re-distribution rights for authors
  • self-archiving rights (of original manuscript etc.)
  • free classroom use etc.

Thanks PNAS – you guys made everyone’s life a bit easier.

Requesting Permissions for Re-use of Copyrighted Material.

Now I am not normally one to rant, at least not on a blog, but today I encountered something that makes me just mad…..and I mean hopping mad.

I have just finished writing a review paper on poly(2-oxazolines)…a class of polymers close to my heart. As it is a review paper, I have included some figures, which were taken from the original research papers forming part of the review. Given that these were not my figures and that I respect and honour the copyright of other authors who have worked hard to produce high-quality and illustrative figures for their publications and the copyright of publishers who have been assigned those rights by an author, I went off to request permissions for re-use of copyrighted material from the relevant publishers. The review was based on about 150 papers, and I had taken figures from a few of them…ACS, RSC…no problem. Their procedures are all more or less automated and relatively pain free, although time consuming. And then, well then I came to Elsevier……

Elsevier has outsourced their copyright clearance procedure to a company called the Copyright Clearance Centre (I have included the link for your edification), which, on its website claims to “help to advance education, innovation and the free flow of information.” So far so good. Following Elsevier’s instruction, the first thing I have to do to obtain permission, is to go and find the resource I took the figure from on ScienceDirect. So off I go and locate the relevant journal (Talanta) and citation on Science Direct. Next, the website instructs me to find the abstract of the paper and to press the “Request Permissions” button.


Pressing this button launches a pop-up window which asks me what I want to do and I make my selections:


I am somewhat curious as to why it asks me which currency area I am currently in, but decide to ignore it for the moment. Having made my choices, I hit the “continue” button. I am then asked to set up an account as I have never used rights link before. Ok, getting tedious, but I hit the button to set up an account (note: none of this is necessary with the other publishers). I am now taken to a page where the anger really sets in: they are asking me how I want to pay.


How I want to pay?? All I want is to request permission for reuse of one small figure. I do not want to pay anything – my institution is subscribing to the journal for me. Why on earth would you want to lump requests for re-use of copyrighted material together with a business process that may be appropriate for the purchase of pay-per-view access? If I do not want to have pay-per-view access, why do I need to hand over payment details? However, the dropdown menu only gives me the opportunity to choose between a credit card payment and an invoice.

Hmmm…..on I go and fill in my details hoping that the “payment” thing is just going to go away down the line. But no such luck and sure enough, on the next screen I am being asked for my credit card details IN ORDER TO BE ABLE TO SET UP AN ACCOUNT to request re-use permissions.


At this stage, I broke off the procedure. I understand that it might be convenient for the “Copyright Clearance Centre” to set up an account for me in such a way, that if I ever wanted to purchase a journal article from one of their customers, they have all the necessary information. IT IS NOT CONVENIENT FOR ME. All I want is permission to re-use a figure in a paper. I do not think that I should have to hand over my credit card details for this and I refuse to do so.

So what is the consequence of this? I am not prepared to set up a Rightslink account with the Copyright Clearance Centre under these circumstances. Therefore I cannot obtain permission to reproduce the figure I wanted and therefore I cannot use the figure in my paper. Furthermore, there is the personal inconvenience: I now have to throw the figure out of the manuscript and to renumber all of my figures in the text. This will cost me at least half an hour.

More significantly though, this has a negative impact on scientific dissemination. On the grand scale of things, it is only a tiny thing, but in effect this has stopped me from re-using a figure created by other scientists, which, I am sure, have a vested interest in their research being talked about, evaluated and disseminated. That is part of a scientist’s core business. The Copyright Clearance Centre has neither helped to advance education and innovation, nor indeed the flow of information, but rather has impeded it. And Elsevier is indirectly guilty: they have not done their best for their authors by helping to disseminate their science, but are collaborating with an organisation which actually puts people off reusing science. They have allowed requests for re-use of material to be lumped into the same procedure used for the purchase of pay-per-view articles. At best that is thoughtless and very poor customer service.

Now as I say, I don’t like to rant, but this kind of thoughtlessness makes me mad.

Photolabile Dendrimers…

…which are in many ways conceptually similar to Shabat’s self-immmolative dendrimers were published by Kevwitch and McGrath in the recent issue of New J. Chem. (DOI: 10.1039/b617289j). These dendrimers contain o-nitrophenyl linkers in the core, which allow the controlled degradation of the material:


The photolabile core can be prepared from piperonal in a relatively straightforward way. As was the case for the self-immolative dendrimers, a trigger event – in this case irradiation – leads to the fragmentation of the dendrimer. In this case, the dendrons detach from the core – no complete unraveling of the architecture occurs.

An elegant synthesis…

…of core-shell brush copolymers has just been reported by Wooley et al. (Macromolecules, 40, 2289 (2007)).<img id="image48"


The exo-norbonene-functionalized raft agent was prepared by esterification of the corresponding alcohol with an acid functionalized raft agent (87 % yield). This was followed by the one pot ROMP and RAFT procedures. The ring-opening metathesis procedure was carried out using a Grubbs catalyst in CH2Cl2 to give a poly(norbonene) derivative with an Mn of 40.6 kDa and a PDI of 1.24.

The RAFT polymerization was then carried out using styrene and maleic acid anhydride as co-monomers and AIBN as the initiator (50 deg C reaction temperature). The comonomer pair was chosen due to their low reactivity ratios, which allows the one-pot preparation of statistical polymers of the type poly(styrene-stat-maleic anhydride)-block-poly(styrene). 1H NMR suggested quantitative conversion of the maleic anhydride after 16 h, but only 8.2 % for styrene. The reaction was allowed to continue for another 16.5 hours and quenched after 12. 8 % styrene conversion to give the desired core-shell brush copolymer (Mn=1200 kDa, PDI = 1.32).