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

Fri Oct 5 09:12:32 UTC 2012

On Fri, Oct 5, 2012 at 10:06 AM, Susi Toma <toma.susi at aalto.fi> wrote:

>  Dear Peter,
>
>
I never tell individuals what they should do - I have the luxury of not
having to worry about h-indexes and tenure committees. If co-authors wish
to publish in closed access journals I won't object.

 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 agreed it was useful! It makes a very strong case for  trying to find a
better solution. And if we can be part of that, great.

>
>  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.
>

I am not surprised. Chemists want people to cite their work but not
necessarily to read it.

>
>  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.
>
> Max Planck.

 In any case, I appreciate the interest and taking the time to answer in
> length!
>
> That's what this list is for!

>  -Toma
>
> "Peter Murray-Rust" <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> 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
>
>

-- 
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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