[open-science] Inside view to the story of an high impact publication

[Susi Toma]

Dear Peter,

Your remarks are welcome and very well taken; perhaps it was an exaggeration to talk about open science (although I did write I'm inspired and not practicing it, but that's semantics).

I wonder what term would be better here? Discussing openly what happens typically behind closed doors and high in the ivory towers of science is surely useful even if it's not strictly open science.

I'll have to tell you that our senior co-authors were not comfortable with even this level of openness, and we had to remove some correspondence from the post on their request.

So we're pushing as much as we can, but what a wise man once said seems to hold still: science advances one funeral at a time.

In any case, I appreciate the interest and taking the time to answer in length!

-Toma

"Peter Murray-Rust" <pm286 at cam.ac.uk<mailto:pm286 at cam.ac.uk>> kirjoitti 5.10.2012 kello 11.42:



On Fri, Oct 5, 2012 at 5:50 AM, Susi Toma <toma.susi at aalto.fi<mailto:toma.susi at aalto.fi>> wrote:
Dear open-science readers,

You might be interested to read a longish blog post I wrote about a recent high impact research article (alas, not open access; let me know if you want to read it and don't have access) I co-authored with Jani Kotakoski. It contains some interesting statistics of the email correspondence as well as inside details of the process, somewhat along the ideals of open science.

http://mostlyphysics.wordpress.com/2012/10/04/the-story-of-an-article/


This is a carefully detailed account of collaboration in authoring a conventional closed access paper. I think many may find it useful.  I think it stresses collaboration, the problems of refereeing and editors, but it isn't similar to open science. So my comments are primarily about that... Please take them as constructive.

In a full open science process the major part of the research would have been posted openly and would potentially have been available to people outside the research group both for reading and comment.

If the open process is restricted to authoring then the manuscripts would have been posted openly. You mention a large  number of emails and Googledocs. Googledocs is a relatively poor vehicle for scientific manuscripts as it has poor version/control and poor reference management. Indeed this is an area where I would like to see open offerings that address these points.

You have submitted to journals (ACS) which will refuse to publish if *any* of the work has appeared in public anywhere. For example, in the distant days when I published with ACS, we published a paper on the CML schema. (This is in the field of cheminformatics and ACS was the only publisher anywhere who would accept papers on this topic - we now have Open Access alternatives.) I asked the editor if we could post the schema for public comment and this was refused. Nowadays I would simply do it. The ACS does not allow Green archival of any sort except in dark archives with large embargo times (probably decades).

Your initial paper - on which I can't comment as there is no public record of it was required by the journals to be bounced around different publishers. It was both too long for some and too short for others and looks like your original paper has been split into two by the journal system. The first, as I understand it, is 4 pages and contains little useful experimental detail - this will be published separately. Is this the best way to publish the science? I don't know since none of the versions are publicly accessible.

The message I take from this is that the journal system puts serious pressures on where and how to publish. In open-science we don't have this problem. We publish to the world and record everything. We (or someone else!) can write narratives on the data.

If we limit this to open-access (i.e. do the science closed but publish openly in conventional journals) this emphasizes the need for a versioned record of the publication. All significant versions should be available for public view and comment. It may be that you would find public support for your original manuscript or you may find there were significant flaws.

This has been a useful example and my suggestion is that this list (open-access) should think about open authoring tools. It's clear that a huge amount of wasted effort is created by the re-authoring process - reformatting, re-doing the reference labels, etc. In OKF we have an emerging toolkit that will address some of these points.





--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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