blogging peer-reviewed articles – icons and greasemonkey

One of the features fo having subscribed to planeScifoo is that I am now getting lots of new feeds. I probably shan’t continue some of them, but here Bora highlights something similar to what the chemical blogosphere has been doing. (Bora Zivkovic: A bloggers’ icon for posts about Peer-Reviewed Research)

A better way for bloggers to identify peer-reviewed research

Category: General / Site news
Posted on: August 8, 2007 10:12 AM, by Dave Munger

Most CogDaily readers are familiar with the little icon we developed to indicate when we were reporting on peer reviewed research. We created it when we began to offer links to news and blog posts, as a way of distinguishing those less “serious” posts from when we were talking about peer-reviewed journal articles.But Sister Edith Bogue of Monastic Musings recently pointed out that other academic bloggers could also make use of the icon, to distinguish when they’re blogging about news, family, books, etc., from serious scholarship. But our icon isn’t ideal for this purpose since its design is specifically linked to our site. I also think a public icon should come with some guidelines for use.
So Sister Edith and I, along with ScienceBloggers John Wilkins and Mike Dunford, have decided to work together to develop such an icon, along with a web site where we can link to bloggers who’ve pledged to use it following the guidelines we develop. But we don’t represent the blogging community as a whole, so we thought we’d also ask for your input. I’ll start the discussion with a few key questions. You can post answers — or your own questions — in the comments section.

  • Is “Report on Peer Reviewed Research” a good tagline? Any suggestions for a different wording?
  • What should we call the organization that sponsors the icon? I was thinking something on the lines of “Bloggers for peer review.” Any other ideas?
  • What, exactly, should the icon signify? At a minimum, the blogger should have carefully read the original research report. Any other guidelines? (On CogDaily, it means that both Greta and I have read the report, and that we’re attempting to offer a thoughtful summary of the results)
  • How do we define “peer review?” For example, some conference presentations are technically peer reviewed, but this process seems to me too cursory to qualify — after all, the reviewers haven’t even seen the final product. Some journals with very limited peer review processes also might not qualify. How do we decide what’s in and what’s out? Do we make a list?
  • Should there be a process for policing abuses of the icon? How would that work?
  • What about copyright for the icon? Should it be in the public domain? Or would some sort of license like the GPL or Creative Commons be better?
  • How should we design the icon? A contest? How would results be judged?

That ought to be enough to get the discussion rolling. As I suggested, feel free to offer both answers and additional questions. This is an exciting project!

PMR: Read the comments as well. My understanding is that this gives a blogger a chance to tag their post as being about a peer-reviewed article (not that the blogger has been certified as fit to blog! – you have to make your own choice about this). In chemistry several of the blogs routinely comment on peer-reviewed articles, some almost exclusively. Have a look at TotallySynthetic’s blog which reviews organic syntheses from major journals. Typical example:

Geigerin

6 August 2007

geigerin.jpg
Deprés and Carret. ACIEE, 2007, EarlyView. DOI: 10.1002/anie.200702031.
Isolated from the plant colloquially known as the “vomiting bush”, Geigerin is a member of the guaianolide family, represented in the 5,7,5 tricyclic structure. No further mention of the biological activity is noted in this paper, but they do point out that this isn’t the first synthesis of this family, referencing Lee and Bartons works.
The synthesis starts with a bit of chemistry quite familiar to the group, doing a regioselective [2+2] cycloaddition with diphosgene 2,2,2-trichloroacetyl chloride and 7-methylcycloheptatriene. In their previous papers, they had to use a metal to take diphosgene to dichloroketene, but in this case, a bit of ultrasound worked rather well. They then ring-expanded to give the 5,7 motif required.
geigerin_1.jpg
A few steps further along, they used DMDO to generate the hydroxyl group with good substrate control, which formed the lactone under acid conditions. To reuse a phrase I type a lot – not new chemistry, but nice!
geigerin_2.jpg

PMR: Notice there are FORTY comments already – I select a few of the early ones (numbering is unreliable)

40 Responses to “Geigerin”

    1. Spiro Says:
      “In their previous papers, they had to use a metal to take diphosgene to dichloroketene, but in this case, a bit of ultrasound worked rather well.”Ultra sound avoids the use of activated zinc (ref 14), but you definitely need a metal.
      Maybe I am wrong but there is no supp info available, as often with Angewandte :-(
    2. aa Says:
      spiro, the supporting info is available at http://www.wiley-vch.de/contents/jc_2002/2007/z702031_s.pdfand i think the procedure for the 2+2 is found in their previous methodology paper,referenced in this one.
    3. Spiro Says:
      aa, thanks for your dedication, but I had read these “supporting information” before writing my discontentment.
      It is just that I do not consider this to be a decent supporting information section, even though the three procedures they show are the most important of the article.
      I do not blame the authors, just the journal. If my boss tells me to write a paper without supp info, I cheer. But this is a bad habit IMHO.
      For example, I am perplex about transformation c in scheme 3, especially when I read ref 19. One way or another there may be something which is missing in the conditions (acid?), and a written procedure could clarify things.
    4. carbazole Says:
      The lack of supp info in ACIEE is really frustrating. If you’ve done a total synthesis, why can’t the supp info include any procedures for making compounds not already found in the literature? If I’m doing a lit search, and I find a reaction in Org Lett that I can use, I cheer because it will have a procedure most likely. If it’s for ACIEE, I groan, because the supp infos are so spotty.
    5. kiwi Says:
      Tropylium tetrafluoroborate is the listed starting material – now thats something you don’t see everyday. I sure hope they weren’t buying it…
    6. Liquidcarbon Says:
      Is it stereocontrolled enolization of methyl propionate that introduces the side-chain stereocenter in the “double conjugate” addition?
    7. Gilgerto Says:
      I totally agree with you carbazole, I cannot conceive that in 2007, a supp. info for a total synthesis includes only 2 procedures and 4 nmr. It is clearly a lack of rigour from Angew…

    PMR: Impressive. Many thoughtful comments here. Close to my own heart is the concern about the lack of supplemental info – the raw experimental stuff. The chemists at the bench are crying out for this and the journal doesn’t provide it. [ACIEE == Angewandte Chemie, flagship chemistry journal from Wiley].
    What Dave Munger and colleagues suggest is that this post from TotallySynthetic carries a little icon *in the post* indicating that the post is about a peer-reviewed article. That’s easy and a good idea as we would have ways of aggregating all these.
    Dave – the chemical blogosphere has taken this idea further with a greasemonkey script that enhances a Firefox view of the original article (Travels of the Blue Obelisk Greasemonkey). This tool works out that the article has a DOI which relates to one or more blogosphere posts and pops up an icon when viewing the TOC. This is completely independent of the publisher. (Whether publishers approve of this – as they should – isn’t technically relevant). Of course the reader has to have the greasemonkey installed but that is almost trivial. In that way you get bidirectional feedback – readers of the blog get pointed to the article – readers of the article get pointed to the review.
    What this means is that the blogosphere can make a complete range of comments on articles. Most of TotSynth’s are complementary – I think he selects articles because they are inspiring rather than flawed. But he and others will certainly criticize articles which are suspect and there has been a fair amount of this over the last year.
    (Good time to mention that Nick Day and I will shortly be announcing a greasemonkey for crystaleye that links to crystal data in publications).

    This entry was posted in "virtual communities", chemistry. Bookmark the permalink.

    5 Responses to blogging peer-reviewed articles – icons and greasemonkey

    1. While the icon is a good idea, the underlying concept is to attach a piece of metadata that
      describes the nature of the relationship between the blog entry and the object of discourse.
      Anyway, I think a more appropriate way to go about this is to either
      1) use a standard tag — is that so much harder than an icon – at least it would be something
      for technorati, and the other blog engines to chew on.
      2) use some sort of micro-format to convey this: in the same way that the favicon is described,
      describe the ‘peericon’.
      Just my .02 cents,
      Rick

    2. The link to ‘Travels of the Blue…’ seems to be broken (two forward slashes before ?p=425). I did find it eventually

    3. Pingback: Science Library Pad

    4. pm286 says:

      (2) Sorry, Cameron. I cut and pasted the link and WordPress sometimes drops some of the address. I’ll mend it.

    5. pm286 says:

      (1)Thanks Rick. I think you are right for mainstream bloggers who use tags and for readers who look to the tags immediately. It’s probably more for readers who appreciate visual prompts.

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