Who’s Guilty? (Photo credit: Wikipedia)
About a year ago, while attending a publishing strategy meeting focused on open access (OA), a couple of OA publishers told me that eLife articles had just been published on PubMed Central (PMC) and were available nowhere else. Given PMC’s protestations that it “is not a publisher,” this situation seemed wrong. More aggravating to these publishers was the fact that eLife apparently received special treatment, avoiding stated requirements before their content was not only included in PMC but actually published originally there. On top of it all, eLife had not yet demonstrated any independent publishing capabilities, since the eLife site had not yet launched.
I wrote about how this looked from the outside and included notes from my initial interview with the Director of the National Center for Biotechnology Information (NCBI) at the NLM, David Lipman (who is also Executive Secretary for the PMC National Advisory Committee). Lipman represented during our conversation last year that eLife had submitted a PMC application using “the regular procedure” while also asserting that he knew nothing about any conversations that might have gone on leading up to the launch of eLife on PMC.
After what struck me as unsatisfactory answers and aggressive stone-walling, I filed a Freedom of Information Act (FOIA) request about a week later. I’ve been receiving documents based on this and other FOIA requests ever since and have published numerous posts on what I’ve received. The final packet responsive to my initial request arrived earlier this month — another 330+ pages of emails and internal documents to pore over. Many documents were familiar, but some expanded on items I’d seen before, while some were brand new and a bit startling.
As an aside, I never anticipated that inquiring about eLife and PMC would yield 859 pages of documentation. Now that the entire request has been fulfilled, the sheer scope of what went on can be appreciated. It wasn’t nine pages or 59 pages — it was 859 pages.
A few things come into sharper focus thanks to these additional documents:
- Lipman was intimately involved in discussions around the inclusion of eLife and its special treatment, from the very beginning through the moment when eLife articles debuted on PMC
- When Lipman disavowed knowledge of what happened leading to eLife publishing its first content on PMC, he was not telling the truth
- Plans to publish eLife articles on PMC were fairly concrete even before eLife secured its ISSN or was able to put up any sort of basic Web presence
- In order to pull off the strange publication process that eLife required, the NLM had to resort to “lying” to its own systems and processes
- Those involved were very clear that this was special treatment for a “friend,” and that they wanted to conceal this special treatment from the community at large
This is a long post in which long email threads are recreated, typos and all.
Let the Games Begin — Again
Last February, I published a post detailing the copies of relevant emails I’d received at the time. As a refresher, on February 24, 2012, Mark Patterson at eLife (then writing from a Wellcome Trust account) pitches the idea of publishing eLife articles on PMC in an email to Ed Sequeira at the NLM, with copies to Lipman and Jo McEntyre of UK PMC.
That same day, in a newly revealed email, Lipman responds to Sequeira:
I’m not sure what Mark has in mind. I don’t see what a preview eLife article is “accepted for publication” that is not simply a published article in eLife. What do you think? They should just start the journal in “preview” mode.
Exactly what “‘preview’ mode” represents isn’t clear. As you’ll see, Lipman has a habit of using quote marks around vague ideas he’s trying to push. Sequeira responds to Lipman about 70 minutes later:
It sounds like they don’t want to launch the journal officially until oct or nov, but they still want to publish articles officially through PMC. Otherwise they could release these on their own site — unless they aren’t ready technically. Sounds weird. I’ll respond and suggest we talk on the phone.
Lipman responds five minutes later:
Maybe if possible I should be on this.
A minute later, Sequeira responds:
If you’d rather respond to him directly, that’s fine with me. Let me know. Otherwise, I’ll copy you on my response so that we can coordinate on a time for a call.
Five minutes later, the thread ends with Lipman replying:
I will respond and cc you.
As noted in the post from earlier this year detailing the first batch of emails about these interactions, Lipman wrote an intentionally vague email responding to Patterson and McEntyre that same day, cc’ing Sequeira. We now have additional emails showing more conversations branching from this thread and showing Lipman’s intimate involvement in setting up eLife on PMC. Three days later (February 27, 2012), Lipman wrote to Sequeira, copying Bart Trawick:
I spoke with Mark Patterson and he had an interesting idea for doing these “preview articles”.
Bart – Mark Patterson is now the Managing Editor for eLIFE (HHMI, Wellcome Trust, & Max Planck Institutes upcoming OA journal). Patterson is interested in having some accepted articles publicly available prior to the formal opening of the journal.
He wanted to simply have peer-reviewed & copyedited articles submitted through the NIHMS system. Then, when the journal is up and running, they would send the OA articles for PMC and for their site. It’s kind of a cool idea.
I realize there are issues for this – for example, there won’t be any pre-existing pubmed records. But can we think of a way to handle this?
NIHMS is the National Institutes of Health’s Manuscript Submission system, which was designed to facilitate the submission of final peer-reviewed manuscripts — you know, the kind that cost NIH $47-50 each to convert into XML and QA. Here we see Patterson trying to create a back door into PMC for eLife papers, and Lipman pushing staff to find a way to make it happen.
Sequeira responds the same day:
It’s a nice idea, but it runs into the common problem we have here: if we do it for one group we have to be willing to do it for others as well and then we have to find ways to shoo away the riff raff. I don’t see how the NIHMS pathway being a factor here one way or the other — unless we’re talking solely about articles funded by our participating agencies: NIH, Wellcome, HHMI.
With the funder qualification, we could create a mini-repository of pre-publication papers. But then the question becomes: how long will this last; will anyone contribute to it after eLife is born; will this be short lived like RRN?
A better option may be to have Wellcome advertise these articles via UKPMC. They already offer content that’s not in PMC. They could just put up abstracts and PDFs and since it’s a Wellcome journal, there’s less of a problem with creating a precedent for every other publisher that wants publicity. If this seems viable, we could think through the details.
Note that Sequeira is clear that eLife’s request is about publicity. Trawick responds to the thread about a half-hour later:
The technical issue from the NIHMS side is that manuscripts are matched to journal records before processing. If the journal record does not exist in the NLM Catalog (not unusual), we kick off a process with LO where they investigate into the legitimacy of the journal, gather the ISSN info, etc, and create the record. Then we match the manuscript to this and processing can begin.
Believe it or not, we have gotten papers from ‘faux’ journals before, including one that was just some guy’s blog.
“LO” is “library operations.” I don’t know what “RRN” is.
In a response to Sequeira’s email above, Lipman shows his hand:
Hmmm – I think there’s still a work-around here because we have a “relationship” with HHMI and Wellcome Trust. If either or both of them “sponsor” these papers, the $ side is covered. Furthermore, if either or both “certify” these papers, then we are covered in terms of setting a precedent with any given journal. Finally, in terms of publisher permissions – as these are OA, there’s no problem there.
So the key issue would be to get LO to accept the legitimacy of ELife.
I think this is still a possibility then – let me know if you want to discuss this more.
The phrases in “quotes” are worth pausing over. There is a “relationship” between PMC and HHMI and the Wellcome Trust. Indeed there is — so much so that the Wellcome Trust was allowed to handpick a successor for the PMC NAC as one Wellcome employee rotated off, and they picked their solicitor to take over this de facto seat on the NAC. When the Wellcome Trust’s solicitor’s term was expiring in late 2012, Lipman wrote in an email to a group trying to drum up candidates:
We certainly want to get someone from elife and I’ll look at that group of editors.
Then there is the use of the word “certify.” Every journal “certifies” papers by publishing them — some more plausibly than others. So how the certification of eLife differs from the certification of any other journal isn’t clear. I think the nice way to say it is that Lipman is being artful as he tries to move the eLife cause forward.
A Brief Interlude As We Contemplate the Concepts of “Fairness” and “Honesty”
I’d like to pause a moment so we can regain our bearings and remind ourselves that two issues at the heart of this controversy are fairness and honesty. To put this into context, I’ll use an unrelated email exchange from June 11, 2012, between Chris Kelly and Sequeira regarding Bentham, an OA publisher:
FYI, we have a pesky Bentham Open editor back asking for reasons why we aren’t taking Bentham journals any longer. No matter what we say now, I fully expect this will turn into a dust up with Matthew Honan at some point shortly . . . but I’m about to rehash Abby’s original response to Urooj from January and hope that gets this guy off our case for a few minutes . . .
I’m in the mood to take a more aggressive / blunt stance here. He says “Obviously, not to be indexed in PubMed will hinder any progress of the journal and as the editor I need to know.”
My response: We do not accept a journal into PMC or PubMed with the idea of helping the journal progress and prosper. We expect the journal to do that on its own. We suggest that you asked Bentham management about their previous communications with PMC. This is not a matter of the quality of a single journal. It is a matter of the publishing practices of the organization overall.
This independent exchange provides some interesting contrast to the eLife and PMC discussions. Entire organizations can get special treatment — special positive treatment or special negative treatment. But most striking, of course, is Sequeira’s claim, contemporaneous with PMC’s moves toward assisting with the launch of eLife, that:
[w]e do not accept a journal into PMC or PubMed with the idea of helping the journal progress and prosper. We expect the journal to do that on its own.
The evidence suggests otherwise, unfortunately. That’s not fair, and that’s not honest.
And Now Back to Our Main Feature . . .
Returning to our email exchanges from February and March 2012 between Lipman, Sequeira, Patterson, et al, we start at a point originally captured in an earlier post. On March 4, 2012, Patterson emailed Sequeira, with a cc to Lipman and Melissa Dodd, head of production operations at eLife (scan of these emails):
I’ve had further discussion with David about using the PMC author submission system to distribute accepted versions of eLife articles before launch of the journal around November of this year.
To enable this to happen, I understand that we have to have eLife included in the NLM catalogue, which in turn requires an ISSN. I’ve applied for an ISSN and will let you know as soon as this is available. Meanwhile, can you let me know of any other information that you’ll need for the purposes of the catalogue?
. . .
Best wishes, and many thanks in advance for your help with this initiative.
Now, we get into a new branch on the same tree. Lipman replies to Sequeira the same day (Sunday) in a separate thread, copying Dennis Benson at the NIH:
I told Mark that if either Wellcome Trust or HHMI are willing to take responsibility for these documents – i.e., as if they funded them, then we can handle the tagging costs effectively drawing from funds they’ve previously provided for tagging. According to Mark, there will only be a dozen or so.
THe notion would be that once the paper is peer reviewed and copy edited, they would use e.g. the HHMI route to upload the manuscript and we’d tag this and return. One eLife is fully in production, they could replace these documents – Jim mentioned that we have some workflow to supercede an author manuscript version with the published version.
Let me know if we need to discuss.
Sequeira responds the next day:
As Mark mentions, the first step is to get an NLM catalog record for eLife. LO would normally require some physical evidence of a journal beyond an ISSN, e.g., at least a skeletal journal site. So we’ll probably have to pull some strings to get the catalog record. Have you spoken with Sheldon or anyone else there about this or do you want us to?
Tagging itself is not an issue. Wellcome could even process these on its end and deposit them via the UKMSS pipeline. In that case the NIHMS doesn’t have to be involved at all.
Normally it isn’t a problem to replace a manuscript with a published version, because the manuscript isn’t released in PMC until the article has been published and we have a proper citation for it. Citation matching can be done automatically.
These articles are quirks. The official citation will be sometime in the future. So at the very least we’ll have to handle the replacements manually. We’ll also have to figure out some creative way of citing them for now — unless eLife is willing to assign them permanent citations now.
A week later, on March 12, 2012, Sequeira emails Lipman with copies to Chris Kelly, Jeff Beck, and Sergey Krasnov:
LO has created a skeletal catalog record for eLife, http://www.ncbi.nlm.nih.gov/nlmcatalog/101579614. We can flesh it out once Mark has an ISSN and the journal information site that he expects to be ready in a couple of months. I’m talking to him later this week about official publication dates and other details for the ‘pre-launch’ articles.
Lipman replies less than an hour later to cheerlead for eLife:
Sounds great Ed – I hope they get overwhelmed with papers. . .
It Becomes Clear That eLife Is Driving the Bus
Three days later (March 15, 2012), Sequeira sends a long and specific email to the team of Kelly, Beck, and Krasnov, adding Sarah Post Calhoun:
For the record, my conversation with Mark today. We agreed to mull over questions about final published version, what’s released in PMC initially, etc. and discuss again in a week or two.
Expect to have a journal info site up in 3 weeks. Will include details about editorial board and editorial / review policies. Online submission site in place by the end of May.
About to apply for an issn. (eLife was incorporated as a non-profit corp in the US but Mark is operating out of the UK, so there was a question of where they get the issn.)
Talking to members of the editorial board about submitting ‘seed’ articles for publication in eLife in the next few months, instead of sending them to Nature, Cell, etc. Focusing on high impact papers; quality over quantity. They may get about a dozen of these in the next 6 to 8 months, but don’t really know at this point. Hoping to have about 50 articles, total, published by year end.
Authors of most of the seed articles will be funded by HHMI, WT, or Max Planck, but there could be some who aren’t funded by any of these three. So there could be some articles that, technically, aren’t HHMI or UKPMC manuscripts.
Need to differentiate between the official start date of the journal — which has to be no later than the date the first article is released in PMC — and the launch of a fancy journal site (with a party, etc.), which they’re hoping will be in nov/dec. Hope to have the first seed articles ready for PMC by july/aug.
Aim to give us the seed articles in final, copy-edited form (emphasis on content; PDF formatting, etc. may not be finalized till later). Still, it’s unlikely that we’ll really have the final, final content in PMC for the seed articles at initial deposit. So I’m thinking we treat the initial deposits as manuscripts in PMC, which can be replaced later by the official published version (even though both will have the same publication / release date).
The official date of publication for a seed article will/must be the day on which it is released in PMC. This means that if we decide to load them as manuscripts in PMC, the manuscripts will have citations in the form “eLife. Author manuscript; available in PMC 2012 July 15. Published in final edited form as: eLife. 2012; 1: e12345. Published online 2012 July 15.”
The final published article will be an illusion at this stage. The physical object won’t exist until later. But citing it will establish the official date of publication and allow us to rationally replace a manuscript with the final published version in PMC eventually. (The illusion becomes reality — or, we’re no longer lying.)
eLife will list the seed articles as published, on its temporary site, when they’re released in PMC. Article citations on the eLife site will take you to the version that’s available in PMC.
Makes sense for them to publish one volume per year with no issues. At the least, it makes it easier to create the proper (final) citation for the seed articles. They won’t need some irregular, sparsely populated, issues. (Mark thought that PMC requires journals to have issues.)
Once the journal is in full production (yr-end 2012) they’re considering immediate release of an accepted manuscript, which will be replaced later by the final, edited version. Other than this, they don’t expect to have versioning.
This email bears some analysis. First, this concrete plan sounds like it was largely dictated to PMC by Patterson, who seems to have been emboldened by his conversations with Lipman. Second, the lengths to which PMC is going to accommodate eLife are extraordinary — basically, fooling their systems across the board in order to help eLife launch sooner and gain a market advantage. The use of words like “illusion” and “lying” is striking. Third, eLife is getting all of this attention at no cost — basically, a custom platform build months in the making is being completed on the backs of US taxpayers.
The attitude of entitlement at eLife doesn’t stop there, unfortunately. As we move from March 2012 to September 2012, things get a little frosty between eLife and PMC, as eLife’s preferred launch date approaches. This email dated September 19, 2012, from Sequeira to Lipman, with copies to Kelly, Krasnov, Jim Ostell, and Peter Cooper, indicates the emerging tensions:
Details on the eLife situation.
Jeff and Chris have been working with the people there for the past two months on tagging of their content for PMC. So far we’ve only seen concocted ‘articles’ intended to test the various constructs they expect to see in real papers.
Yesterday they told us that they would get us files for 8 real articles on Friday (9/21) and that they’d like to have the journal go live in PMC on Oct. 3. When Jeff told Mark Patterson last week that we can’t guarantee processing times until we’ve seen real articles, Mark apparently got a bit testy. Back in March, Mark expected to have the first articles ready to publish in July/Aug and their full-fledged journal site live in Nov/Dec, so he’s probably under pressure to get something out now.
We’d like to have two weeks after getting clean files to get the journal up in PMC. They’ve said that the first batch of articles will consist of four research articles, three insight articles and an editorial. I think we need alll of them at a minimum in order to make this look like a ‘real’ journal and not just a PR effort we’re doing on behalf of our friends.
I’d also like to make sure that whatever they say in their press release makes it clear that these articles in PMC are the first officially published articles for the journal, i.e., this is the launch of the journal even if their own journal site isn’t going to be ready for some months. A note I have from a phone conversation with Mark in March says “eLife will list the seed articles as published, on its temporary site, when they’re released in PMC. Article citations on the eLife site will take you to the version that’s available in PMC.”
Incidentally, Jennifer McLellan asked Neil last week whether we’d like to co-sponsor their press release. I said no, we don’t want to make it look like we’re doing something special for eLife. (message attached)
Let me know if you need more info.
About 45 minutes later, James Ostell, who was included on Sequeira’s email to Lipman and who is Chief of the Information Engineering Branch of the NCBI, replies to the entire chain:
They are giving us less than two weeks to set up a new journal in PMC based on content we have never seen. I think that is pretty cheeky, especially since they are behind in their deadlines and asking us to go early on ours.
There are more emails in this thread, alternating between disbelief at how “cheeky” eLife is being and confidence that they can get it done nonetheless. It’s interesting to watch this UK-based publisher pushing US government employees around so blithely, spending US tax dollars with impunity.
The night of the same day, Lipman emails Patterson:
I was chatting with Ed Sequeira about the first few eLife articles and it sounds like we should touch base by phone to discuss this. As I understand things, you want the articles to go live by Oct. 3 however we still don’t have the articles. It’s difficult for us to promise that kind of turn around so we should chat briefly ASAP. If we have the articles e.g. by tomorrow and there are no issues, then it may be possible to have them ready by October 3. So let’s chat ASAP.
Patterson replies the next morning:
I’m in Budapest at the moment, so it’s going to be tricky for me to speak until I get home. I could definitely chat on Saturday if you’re around/don’t mind. I’ll touch base with the folks in Cambridge in the meantime.
I completely understand if we haven’t built in enough time in the process, and we should err on the side of caution to make sure it all looks good. And let me say too, that Ian and Melissa have really appreciated the help and flexibility that your guys at PMC have offered to us – it’s been great!
I might be able to step out of the conference in the afternoon today or tomorrow to skype, but the other problem is that the internet connection here is s**t.
Lipman forwarded this thread back to Sequeira, Kelly, Krasnov, and Beck:
So Mark seems more calm now. Keep me posted and let me know if you want me to do anything.
In case there was any doubt that Lipman was involved throughout this process, from the initial discussions through to hand-holding eLife during the final steps, we can now lay those doubts to rest — despite Lipman’s initial and demonstrably false assertions that he didn’t know anything about the details of what happened to cause eLife articles to appear on PMC early.
And if there was any doubt as to which group was catering to which, it’s clear PMC was catering to eLife at this time, taking favoritism to some pretty extreme lengths.
More About PR Efforts
One of the most memorable quotes from the earlier batch of eLife and PMC emails came from Sequeira, who wrote in an email about edits to the eLife press release:
Thanks for letting me have a look at this. . . . My reaction to the editorial: Now that we know for sure that you love us, we’d like you to pretend that we’re complete strangers in public.
In an email from the day before these memorable lines were written, Sequeira writes to his internal staff (Kelly, Krasnov, Beck, and Cooper):
At Jeff at least knows, I’m concerned about how eLife presents its ‘launch’ in PMC. The wrong slant provides fodder for everyone from the mystery journals we reject to people like [redacted in source document]. I mentioned this concern when I talked to David the other day and he wasn’t too concerned about it.
Let me know what you think. Am I over-reacting? I’ve made a bunch of edits to their editorial. I’m not expecting them to use my exact words, just trying to convey a change of tone. The differences may be too subtle to matter, so I’d like your opinions before I respond to Mark or say anything further to David.
Krasnov’s reply starts another interesting exchange, and shows the general lack of comfort with the approach to eLife that permeates many exchanges:
Ed, I think your version is the best what we can do.
Do we have an answer on the question – who could this journal pass PMC acceptance criteria?
How could it be accepted for NLM collection (was it?) with zero articles published?
Can we explain it?
We are going to tighten up PMC acceptance criteria but this one is a bad precedent for US government agency. Am I missing something?
Sequeira responds a few hours later:
This is definitely an exception, but I think we can justify the selection for the NLM collection prior to any articles being published. See attached correspondence with LO. NLM has done this sort of early selection with other high profile journals. David’s influenced helped but it’s a lot different from what we did for BMC. I was never comfortable with how we handled them. I’m fine with eLife as long as they don’t present the release in PMC as some kind of pre-launch. That was my agreement with Mark.
This reference to “what we did for BMC” is hinted at again in another email chain starting on October 16, 2012, just a day after the eLife articles went live on PMC. The thread has Sequeira seeking advice about developing a statement to respond to complaints. Judith Eannarino writes the last message on the thread:
Ed: Minus the last sentence, the response looks fine.
Working group: Just to review — in general, NLM only rarely makes special arrangements to accept forthcoming content; indeed, the only other title that comes to mind is PLOS Currents. In addition, NLM has given BMC journals preferential treatment in a number of cases, accepting several titles that do not yet meet the current 6 month/30-paper criterion.
We’ve seen Eannarino before — she is the LO individual who gave eLife a “what the crap” record number in order to grease the skids for it.
There are a few points to pull out of this message. First, special accommodations are made supposedly based on the credentials of the publisher — but eLife had no credentials at this time other than funder credentials (which are not publisher credentials), while PLOS and BMC credentials certainly pale compared to those of major society or commercial publishers with 100+-year track records, many of whom were at the time waiting to get their OA content into PMC and thereby into PubMed. Second, if BMC (which was founded by Lipman’s friend Vitek Tracz, the man who also hired Lipman to edit a journal at BMC) received some form of special treatment sufficiently beyond the pale to leave an uncomfortable memory in employees minds, and then F1000 Research, another Tracz product, received its own special treatment this year, what are we to think about conflicts of interest and fair play?
While this appears to be “more of the same,” it is both a lot more of the same — creating a more comprehensive picture of the duplicity and favoritism practiced at PMC around eLife and potentially other publications — and it is in some ways new. The new information includes:
- insights into how uncomfortable NLM staff was with the way eLife was being handled
- documentation of how involved Lipman was end-to-end and at a detailed level in launching eLife on PMC
- evidence of how much PMC catered to eLife’s whims
- emails showing how funders like Wellcome and HHMI are viewed by government employees working on PMC
- clues that the conflicts of interest between Lipman and Tracz may go deeper (and further back) than we’ve previously thought
Overall, these emails provide yet another eye-opening, embarrassing, and disappointing portrait of PubMed Central management.