Friday, April 02, 2010

Bipolar Electrodeposition of CdS: Scientific Results in Limbo?

There has been a lot of discussion about the fear of getting "scooped" as a reason to be weary of using new scientific publication vehicles.

These conversations can be somewhat frustrating since people don't necessarily use the same definition of that term. Even dictionaries don't use the same language. For example, has:
to get the better of (other publications, newscasters, etc.) by obtaining and publishing or broadcasting a news item, report, or story first: They scooped all the other dailies with the story of the election fraud.
Wiktionary has:
To learn something, especially something worthy of a news article, before (someone else). The paper across town scooped them on the City Hall scandal.
Depending on the definition used, one could argue that in the story I'm going to tell I got scooped or I did the scooping. Some people use the term to imply that a malicious act has taken place. The classic scenario is that one would blog about their research and a nefarious individual would appropriate their results and submit as their own for publication in a peer reviewed journal.

That isn't scooping - it is fraud - and I want to be clear that this is not what I am suggesting happened here.

Two months ago I was asked to review an article for the ACS journal Langmuir. Before 2005 one of my main research areas was bipolar electrodeposition and so I still get asked periodically to review papers in that field.

Not only was this paper in that area but it reported on exactly the same experimental design we had previously reported: the bipolar electrodeposition of cadmium sulfide. The solvent, reagents and substrate were different but it was the same material made by the same process.

Although 2 of our papers were listed in the references the key report was not. I noted this in my review but I was surprised to find that the paper was published without that correction. I contacted the editor of Langmuir to find out what happened. I thought perhaps the authors disagreed with some technical issue in our report.

But what actually happened is that the authors requested that the reference be included in the supplementary data section instead of the regular reference section of the article because it was not a peer-reviewed article. The editor thought that was a reasonable request and complied.

I was quite surprised by this because Langmuir - or ACS journals in general - do not have a formal policy on requiring references to be peer-reviewed. In fact, a quick search for "unpublished results" on Langmuir reveals many articles which use that as an acceptable reference.

I could understand not wanting to cite a blog post with unsubstantiated claims but the document in question is very thorough - it includes a systematic review of prior art, detailed experimental description and characterization data.

This is actually an example of a "SMIRP Knowledge Product". It is a publication device that I used to make public single experimental results from work that was recorded by my research group in the SMIRP Knowledge Management System we used at the time as a laboratory notebook.

The system was built on interlinked modules designed to produce "Knowledge Products" based on a combination of manual and automated workflows. For example, the module generating reviews of prior art was based on "Knowledge Filters" uncovering the novelty of the experiment in question by filtering precedents for relevant aspects.

In the case of "Bipolar Electrodeposition of Cadmium Sulfide onto a Tip of a Carbon Nanotube", the relevant knowledge filters were "Bipolar Electrodeposition", "Electrodeposition onto Carbon Nanotubes" and "Electrodeposition Approaches to Synthesize Cadmium Sulfide". Other modules generated the experimental description, results, discussion, conclusion and reference sections. In this way, not only could the experiment be fully documented but its context within the field could be extremely well defined in a systematic way.

With a workflow to create these knowledge products we still needed a way to communicate them. Back in 2003 options were far more limited than they are now. But luckily (or so we thought) at this time Elsevier was running the Chemistry Preprint Server. They offered a place to upload documents such as these and provided a way of citing them. We used the recommended citation format aggressively, including peer-reviewed articles such as this one from Springer.

However, attempting to access these documents today using the official links gives this as a result:
In what is probably one of the worst scientific publisher PR moves in recent memory, Elsevier broke all the hyperlinks they told their authors to use for citations. If you do some research you will find that the documents are still available from but you have to register to even perform a search to find them! This requirement removes them from indexing by Google. Coupled with the broken citation links these documents are now very far removed from likely discovery.

The story would have ended there were it not for redundancy. I also uploaded copies to Drexel's institutional repository (DSpace), which are happily very well indexed by Google - and perhaps more critically - by Google Scholar. I had not fully appreciated the value of institutional repositories until I noticed that they are treated by some important databases as collections of scholarly works.

So what are the lessons for all the stakeholders?

For those who have scientific results that can be published as articles and MUST be published in ACS journals - send your manuscripts in. If you post them on your institutional repository first they may end up in limbo -they DO qualify as publications preventing you from submitting them as manuscripts to ACS journals - and they may NOT qualify as publications when you try to cite them in ACS journals.

But what about scientific result that cannot be published as manuscripts. The Knowledge Products are unlikely to be accepted by regular journals for several reasons. First they communicate only a single experimental result. Articles generally require narratives. Second, if some of them do get published in traditional journals, there will be copyright conflicts. The Knowledge Filters for the review of prior art will be identical for similar experiments. For example the Knowledge Product for the "Bipolar Electrodeposition of CdS on one Tip of a Carbon Nanotube" Will have identical prior art to the "Bipolar Electrodeposition of Cd on one Tip of a Carbon Nanotube" except for the section of the electrodeposition of Cd or CdS. And no - I don't think it is a good use of my time to move words around for every document to get around copyright issues.

Some of the Knowledge Products were incorporated into full articles when it made sense. But many, including the one under discussion here was not. So publishing this work as part of a full article was never even an option. There are so many scientific results like this that fall into that kind of limbo. Even today there are no really good publication vehicles for these types of results - besides institutional repositories. PLoS ONE might come to mind as an option but I don't think it fits their mandate to publish single experiments like this. And if they did it would be extremely expensive if they did not waive author fees every time. ChemSpider Synthetic Pages and similar initiatives might work for organic chemistry but this is materials science.

Considering all of these difficulties over the years is really the main motivation behind our migration away from a login based system like SMIRP to our adoption of Open Notebook Science based on a wikis and blogs, which are very efficiently indexed in real time by Google and thus easily discoverable without additional formatting work.

For publishers and authors, do you really think it is in your best interest to have a statement in the introduction about prior art say "To our knowledge, reports of bipolar electrodeposition of compounds have not been previously published." when a simple Google search shows that is not the case for the compound you are electrodepositing? I suppose the argument is that the term "published" is used with the technical interpretation of being "published under peer-review". It would have been better to at least make that explicit to avoid confusion. But the bottom line is that someone wanting to perform bipolar electrodeposition of cadmium sulfide will quickly find both reports and will learn two ways of doing it.


At 3:04 AM, Anonymous Henry Rzepa said...

The post raises many interesting issues. One of which is whether deposition of any result into a (DSpace) digital repository prior to attempted publication in an ACS journal might render it ineligible for publication there.

In practice, this does not (has not hitherto) happen. We have now published about 14 ACS articles containing what they call a data WEO. These all contain explicit references to the original Dspace entries, every one of which obviously predates the article itself. This represents 100s of previously "published" calculations. I presume some 30 or so referees, and around 6-7 journal editors at the ACS have seen this. Not a single one even hinted that the article might be invalidated as a result, and in each case, publication has gone ahead unhindered. This attitude has also been taken by Science, Nature, and the RSC.

I would now suggest that "prior precedent" would make it very difficult for these publishers to change their policy at this stage. On the other hand, lawyers are a strange form of iife, and one can never tell!

At 5:43 AM, Blogger Jean-Claude Bradley said...

Thanks Henry - I posted a reply on FriendFeed:

At 1:27 PM, Anonymous Henry Rzepa said...

Another related observation. Can one cite a blog post as part of a more conventionally published article? I decided to test the waters myself on that one. I worked out a scientific hypothesis in preliminary form on both Bachrach's and my blog and then decided to mature it in the form of a peer-reviewed article. This has now been published, as DOI: 10.1038/NCHEM.596

This process was carefully checked by the editor, and the referees, and accepted. It appears therefore that a blog is regarded as more akin to a preliminary conference announcement rather than a publication. Furthermore, the expectation would be that if a blog post really has scientific merit, its author will in fact be expected to put the ideas and the evidence for them through the more conventional anonymous peer review system (which arguably is often broken) in addition to the public review of a blog in the form of comments such as these.

At 1:40 PM, Blogger Jean-Claude Bradley said...

So far we have had no problems using blog posts (or wiki pages) as references in peer reviewed papers. Some journals use Webcite to make sure the content on the page does not change - see for example: Chemistry Central or JoVE

At 4:01 PM, Blogger Cameron Neylon said...

...and I have a couple of blog posts that have been cited more than some of my papers (not that that is all that hard in some cases)

At 4:13 PM, Blogger Jean-Claude Bradley said...

Thanks Cameron - I think bringing up specific examples can help convince people that it can and is being done


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