Open grant writing. Can the Chemical Blogosphere help with "Agents and Eyeballs"

In the current spirit of Openness I’m appealing to the chemical blogosphere for help. Jim Downing and I are writing a grant proposal for UK’s JISC : supporting education and research – which supports digital libraries, repositories, eScience/cyberinfrastructure, collaborative working, etc. The grant will directly support the activities of the blogosphere, for example by providing better reporting and review tools, hopefully with chemical enhancement.
The basic theme is that the Chemical Blogosphere is now a major force for enhancing data quality in chemical databases and publications, and we are asking for 1 person-year to help build a “Web 2.0”-based system to help support the current practice and ethos. The current working title is “Agents and Eyeballs”, reflecting that some of the work will be done by

  • machines, as in CrystalEye – WWMM which aggregates and checks crystal published structures on a daily basis.
  • humans as in the Hexacyclinol? Or Not? saga. Readers may remember that there was a report of the synthesis of a complicated molecule. This was heavily criticized in the blogosphere, and indeed the top 9 hits on google for “hexacyclinol” are all blogs – the formal, Closed, peer-reviewed paper comes tenth in interest.

Given enough eyeballs, all bugs are shallow” – Eric Raymond. In chemistry it is clear that the system of closed peer-review by 2-3 humans sometimes leads to poor data quality and poor science. We’ve found that in some chemistry journals almost every paper has an error – not always “serious”, but … So:
“Agents and eyeballs for better chemical peer-review”.
Not very catchy but we’ll think of something.
It’s unusual to make your grant proposal Open (and we are not actually putting the grant itself online, especially the financial details). But there are parts of the case that we would like the blogosphere to help with. If you have already written a blog on any of the aspects here, please give the link. You may even wish to write a post

  • showing that the blogosphere is organised and effectively oversees all major Open discussion in chemistry. I take Chemical blogspace as the best place for a non-chemist (as the reviewers will be) to start.
  • show that the Blogosphere cares about data. Here I would like to point to the Blue Obelisk and the way Chemspider has reacted positively to the concerns about data quality
  • show that important bad science cannot hide. I would very much like an overview of the hexacyclinol story – which is still happening – with some of the most useful historical links. Anything showing that the blogosphere was reported in the conventional chemical grey literature would be valuable.
  • Open Notebook Science.

We have three partners from the conventional publishing industry – I won’t name them – who have offered to help explore how the Agents and Eyeballs approach could help with their data peer review.
You might ask “why is PMR not doing this, but asking the blogosphere?” It’s precisely because I want to show how responsive and responsible the blogosphere is, when we ask questions like this.
There is considerable urgency. To include anything in the grant we’ll need it within 36 hours, although contributions after that will be seen by the reviewers. I suggest that you leave comments on this post, with pointers where necessary. Later I suspect we’ll wikify something, but it’s actually the difficulty of doing this properly and easily that is – in part – motivating the grant.

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6 Responses to Open grant writing. Can the Chemical Blogosphere help with "Agents and Eyeballs"

  1. Peter, I’ve placed some pointer to past blog items from my blog that I feel relevant [1]. I’ve also tagged this overview with ‘pmrgrantproposal’ and requested others to do the same.

  2. Peter, you don’t half set yourself steep targets with a 36 hour deadline starting on a Sunday morning! My posts on open notebook science are at

  3. Steven Bachrach says:

    Not to splash cold water on this, but one should keep in mind that the cyclohexinol story blew up because of Rychnovsky’s paper in a closed access journal (Org. Lett.). Ruchnovsky chose not to post this in a blog or even in an OA journal. The blogosphere only then picked up on it, and did greatly promote this subject to a wider audience. I think we are still a long way from web 2.0 being the publication access of choice for chemists for original research. For the time being, web 2.0 seems to be more suited as a more personal, chatty style of communication – sort of a hipper, more broadly authored, and more current version of Chemical and Engineering News (or Chemistry in Britain).

  4. Peter, I’ve given many examples of the issue of Data Quality on the blog. Some links are:
    Also, today at the PubChem “Advisory Group” meeting I will be presenting on this issue to the attendees. I will put the presentation online later.
    You should be aware that issues of Quality are showing up already and proliferate problems…for example, while the story about structure drawing quickly is “interesting” the problem is that the structures shown there have errors (at
    It’s good to know that you appreciate our efforts around Data Quality. I’ve never seen a response to my data quality comments on your blog and I assumed that you would have been very interested in the work I’ve done on Wikipedia and taxol validation this past week. FYI, the link back to PubChem and the systematic name have now been edited on the DrugBox and the Wikipedia record is now correct.

  5. Regarding hexacyclinol…I’ve been in the middle of that work and have just finished the manuscript to submit to J Nat prod. Will go in this week. The work has been blogged about at a certain level on the ChemSpider Blog but the full manuscript will go to J Nat Prod for peer review. My experience to date is that my OWN publications receive a more critical eye from non-Open Access journals (but it is a very small dataset out of over 100 publications) and, truth be known, J Nat Prod is the journal to tell the story about hexacyclinol in in terms of our work. Steve is right…while the blogosphere did talk a lot La Clair’s work, there was a lot of mockery of him rather than definitive science around hexacyclinol. Maybe it is out there in the blogosphere..but I don’t know where it is. (My apologies for not recognizing someones scientific commentary if it is there but the efforts should be on reviewing the science and not the person/organization. La Clair was hit real hard..
    The review of La Clair’s synthesis was initiated, as Steve says, in a closed journal. Excellent work by Rychnovsky by the way.

  6. Pingback: Unilever Centre for Molecular Informatics, Cambridge - Jim Downing » Blog Archive » Agents & Eyeballs

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