Eisen Resigns in Disgrace Over Scandal #FSN #PLoSTitution

By Saul Jacobson and Frank Tepedino, Asociated Press Writers

(03-13-2008) 19:50 PDT San Francisco (AP) —

In a startlingly swift fall from grace, the new Academic Editor in Chief of PLoS Biology Jonathan Eisen resigned Wednesday after getting caught in a pay-for-access scandal that made a mockery of his straight-arrow “open access only” image and left him facing the prospect of criminal charges and perhaps permanent exclusion from journal editorial boards.

I cannot allow my private failings to disrupt the people’s work,” Eisen said, his weary-looking brother and Public Library of Science (PLoS) founder, Michael, standing at his side, again, as the closed access-fighting scientist once known as Mr. Open Access answered for his actions for the second time in three days.

He made the announcement without securing a plea bargain with NIH prosecutors, though an NIH official said the former PLoS Academic Editor in Chief was still believed to be negotiating one. The official spoke on condition of anonymity because of the sensitivity of the case.

Eisen will be succeeded on Monday by Alex Gann, a fellow scientist who becomes PLoS Biology’s first foreign-born Academic Editor in Chief and the nation’s first legally blind chief editor.

The resignation brought the curtain down on a riveting three-day drama — played out, sometimes, as farce — that made Eisen an instant punchline on science blogs and fascinated Americans with the spectacle of a crusading scientist exposed as a hypocrite.

His dizzying downfall was met with glee and the popping of champagne corks among many on Crinan Street, where Eisen was seen as a sanctimonious bully for attacking high prices and abusive access practices in the publishing industry when he was a rising Academic Editor at PLoS Biology. And his resignation brought relief at PLoS headquarters in San Francisco after days of excruciating tension and uncertainty.

Some rules can’t be broken, and when they are broken there are consequences,” said Harold Varmus, an Open Access advocate and ex-head of the NIH. “In this case, one of the most promising careers I’ve seen in a generation.”

The scandal erupted Monday after NIH officials disclosed that a wiretap had caught the 39-year-old father of two spending thousands of grant dollars on journal articles about evolution at a fancy Washington hotel on the night before Darwin Day.

Investigators said he had arranged for a journal editor named Kristen to take the train down from New York while he was in the nation’s capital to testify before a congressional subcommittee about the publishing industry.

Late Wednesday, the New York Times reported that her real name is Emma Hill. She declined to comment when asked by the Times when she first met Eisen and how many times she had helped him purchase and download closed access journal articles.

It was unclear whether she would face charges; attorney David Bora confirmed that he represents the same woman in the Times story but wouldn’t comment further.

With every development, it became increasingly clear that Eisen, politically, was finished.

NIH enforcement officials said the Editor in Chief — the scientific heir to the PLoS banner — had spent multiple entire evenings downloading articles and had spent tens of thousands of grant dollars, and perhaps as much as $80,000, on high-priced Nature articles which cost as much as $35 each.

Senior Eisen aides, speaking on condition of anonymity because of the sensitivity of the matter, said Eisen had been informed Friday by NIH prosecutors that he was linked to the grant money laundering ring.

They said he had kept it to himself through Saturday night, when he attended the annual dinner of the National Academy of Sciences in Washington. That night a reporter kept calling cell phones of Eisen aides.

Eisen first shared the news Sunday with his brother at his house in Davis, and after several excruciating hours they told their family, the aides said. By Sunday evening Eisen had called top advisers, personal friends and PLoS loyalists. The little band huddled in the house until midnight.

After making a watery-eyed, non-specific public apology Monday with his brother by his side, Eisen continued to talk to family and advisers through Tuesday. By Wednesday morning, aides said, he had decided to resign.

He and his brother rode in a black SUV from the Davis house to PLoS headquarters in San Francisco to announce his resignation — a trip whose every move was captured by TV helicopters. During the news conference, he and his brother stood inches apart, never touching as they entered or left the room.

Speaking in a strong and steady voice, he apologized for his actions and said: “Over the course of my public life, I’ve insisted, I believe correctly, that scientists regardless of their position or power take responsibility for their conduct. I can and will ask no less of myself.

He did not address the allegations in any detail in the less than three-minute statement, and left without taking questions.

Officials said that Gann asked for the Monday hand-over because he needed more time to prepare and wanted Eisen to say the proper goodbye to his staff.

In a statement issued after Eisen quit, NIH Attorney Lisa Coffmancini, the chief grant money abuse prosecutor in California, said: “There is no agreement between this office and Eisen relating to his resignation or any other matter.”

Among the possible charges that law enforcement authorities said could be brought against the former editor in chief: soliciting and paying for journal access; violating the Consolidated Appropriations Act, the 2008 federal law that makes it a crime to publish NIH funded research in non Open Access journals; and illegally arranging cash transactions to conceal their purpose.

Eisen, a graduate of Harvard University and Stanford graduate school, could also be disdoctorated. In California, a scientist can lose his license to practice for failing to “conduct himself both professionally and personally, in conformity with the standards of conduct imposed upon members of the scientific community.”

It was a spectacular collapse for a man who cultivated an image as a hard-nosed scientist hell-bent on cleansing the state of corruption in scientific publishing. He served four terms as an Academic Editor at PLoS Biology, earning the nickname “Sheriff of Open Access,” and was elected Academic Editor in Chief with a record share of the vote in 2008. The tall, athletic, square-jawed Eisen was sometimes mentioned as a potential candidate for president of the American Academy of Publishers.

But he also made powerful enemies, many of whom complained that he was abusive and self-righteous.

I really don’t feel vindicated,” said Philip Campbell, the Editor in Chief of Nature who lost many papers to PLoS Biology via Eisen’s efforts. But he added: “One of the many things I said was that Jonathan Eisen had one set of rules for himself and one set for everyone else. I never would have imagined it could be so glaring.”

Publishers on the floor of American Academy of Publisher’s annual meeting were transfixed by TV monitors broadcasting Eisen’s resignation, and his ruin drew scattered applause from publishers as they went about buying and selling articles. One said some firms even cracked champagne open — a ritual usually reserved for when subscription fees hit a milestone.

Gann said in a statement that he was saddened, but added: “It is now time for PLoS to get back to work as the people and scientist expect from us.

Barely known outside of his Cold Spring Harbor political base, Alex Gann, 53, has been in publishing since his election to the Nature editorial board in 1985.

Though legally blind, he has enough sight in his right eye to walk unaided, recognize people at conversational distance and even read if the text is placed close to his face.

While Eisen was famously abrasive, uncompromising and even insulting, Gann has built a reputation as a conciliator, and lawmakers quickly embraced the new order.

The first thing he can and I think he will do is end the era of accusation and contempt and ridicule,” said PLoS Co-Founder Pat Brown. “I think everyone will be better off because of it.”

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With apologies to those mentioned above and thanks to the real Associated Press story about Governor Spitzer by Verena Dobnik and Michael Gormley

Wall Street Journal on Open Access

There is a nice essay (Information Liberation) by Daniel Akst in the Wall Street Journal on Open Access to scientific publications (thanks to Bora for pointing this out). He leads of the essay saying

If your child has a life-threatening disease and you’re desperate to read the latest research, you’ll be dismayed to learn that you can’t — at least not without hugely expensive subscriptions to a bevy of specialized journals or access to a major research library.

Your dismay might turn to anger when you realize that you paid for this research.

Go to the WSJ site to read the rest but he has some useful points about OA including:

  • That academic societies and their journals should be able to survive even if they provide the publications for free
  • That “barriers to the spread of information are bad for capitalism”
  • That open access can help limit plagiarism (by allowing anyone to search for copied text as has been done recently for a variety of literary works)
  • That open access to information can help speed development in impoverished nations
  • And his final point: “The challenge, in the coming new world of open access, will be keeping the best of the current system while jettisoning the rest. Maybe some scholar would like to study the question — and publish his findings for all to see.”

Open Evolution

I am starting a new blog theme here on Open Evolution. By that I mean, evolutionary biology studies that are in some form of open science format. This would include Open Access evolution publications, open source evolution programs, open data on evolution projects, etc.

Today I am focusing on Open Access publications with interesting Evolution themes.

First, there are some fully Open Access journals with a specific focus on Evolution (I found some of these through the Lund Univeristy’s Directory of Open Access Journals). These include

There are of course other fully OA journals that have a decent chunk of the papers on some evolution related topic:

If anyone knows of any other Open Access evolution journals, please let me know.

Genomics Blogger Dissed by the New York Times

Well, the New York Times has an article today on Knome, a company that is charging people $350,000 to have their genome sequenced. They have two people signed up so far. Amy Harmon, the author of the Times article, interviewed me by email for her article, mostly because I had blogged extensively about the recent AGBT meeting where many of these sequencing companies had presented their latest goodies. But alas, being a genomics blogger apparently does not carry as much weight as being (1) Jim Watson (2) someone who pays 350,000 to have their genome sequenced (3) running a genome center (Richard Gibbs) or (4) starting Knome (George Church). And so my quotes got left on the proverbial cutting room floor. Go figure.

Too bad for the Times, as I think I my quotes were pretty good. Although in all honesty, they would not have gone too well with the final article, which has some nice cohesion to it.

I should note that, other than the lack of my quotes, one thing that got left out of the Times article is any discussion of the quality of the genome sequence that will be provided by Knome. One would hope that 350K would buy a high quality genome sequence but it is unclear how good it will be. I note they claim they will provide analysis of the genome too, but as with other companies that cater to the rich and famous, details are limited on their web site.

This reminds me of a funny scene I witnessed involving Craig Venter and a wealthy friend of his. This was the day before Craig’s personal genome was set to come out in PLoS Biology and the friend was asking Craig what it cost to sequence his genome. Craig said something to the effect of “man millions of dollars” and then Craig said, “but now it would cost only about 300K.” The friend was intrigued. And Craig asked if he was interested and the friend, without seeming in any way to be joking, said, “sure sign me up.” I guess, when money is abundant, why not get your genome sequenced? Maybe I should have told Harmon this story — then I might have gotten in the Times.

Cool new tool to help decide where to submit a scientific paper and what scientists are working on

Just found out about a freaky and cool new tool called Jane – the Journal/Author Name Estimator. For more on the approach see this paper in Bioinformatics.

Here is how it works — you paste some text into a box and you can get the tool to suggest a journal that is most suitable for your work. Or you can have the tool search for an author who is doing work similar to what is in the text (this is useful to find reviewers or papers to look at)

One thing I like about the journal tool is that it highlights which journals are Open Access and which are deposited in Pubmed Central. I have tried it out in a few different ways and it seems pretty useful. So if you want guidance on where to submit a paper or who might make a good reviewer of a paper, check it out. It seems like it would make a good tool to help reporters find someone to interview too.

The iPlant Collaborative – a new (and seemingly cool) collaborative informatics project

Just found out (from Steve Rounsley) about what seems to be a cool collaborative computational project on plants – the Iplant Collaborative. From their site:

The iPlant Collaborative (iPC) is a distributed, cyberinfrastructure-centered, international community of plant and computing researchers enabling new conceptual advances through computational thinking, and addressing an evolving array of the most compelling grand challenges in the plant sciences and associated, cutting-edge research challenges in the computing sciences.

For more info got to their web site. Also – they are having their 1st conference which apparently will be webcasted. So apparently anyone can watch.

iSEEM Wants You — We are Recruiting Post Docs in Metagenomics Informatics

I am pleased to announce that a new project on “Integrating Statistical Evolutionary, and Ecological Approaches to Metagenomics (iSEEM)” is getting up and running. The iSEEM Project, funded by the Gordon and Betty Moore Foundation, takes an integrated, interdisciplinary approach to metagenomic analysis.

The project spans three labs (mine and those of Katherine Pollard (who is in the Davis Genome Center where I am) and Jessica Green (who is at U. Oregon)), each with different areas of focus. Overall, the plan is to develop and apply novel methods for analyzing metagenomic data with a focus on three main topics: phylogenetic characterization of organisms, ecological diversity, and population genomics. We will be posting more detail about the project at http://iseem.org.

We are seeking five post-doctoral scientists and a bioinformatics engineer to work on methodology for analysis of metagenomic data as part of this collaborative project. Each position will be associated with one of the PIs at their home institution. If you are interested in microbial diversity, metagenomics, or genome evolution, and are looking for a post doc and want to be part of a interdisciplinary collaborative project, please apply.

More detail on the jobs is below:

Qualifications

  • We are looking for people with a demonstrated interest in working at the interface between the quantitative and biological sciences. We will offer a generous salary and benefits commensurate with experience.
  • Postdocs: Applicants should have a PhD in a biological, computational, mathematical, or statistical field. Programming skills are highly desirable.
  • Bioinformatics Engineer: Applicants should have substantial experience with database programming (e.g. SQL), scripting (e.g. Perl or Python), and bioinformatics tools.

Term: Appointments will last 2 years beginning in Summer 2008.

To Apply: Please apply using our online application system. You will be asked for:

  1. a brief cover letter explaining your background, career interests, and preferred geographical location for work (if any),
  2. CV (including publications),
  3. names and contact information for three references.

Online Application System:

Punctuated equilibrium of my blog … and a look at an old science rap

Well, with my new role in PLoS Biology as Academic Editor in Chief, I had planned to start blogging more about PLoS and PLoS Biology. And I will. However, I am going to have to do a half effort on this for at least a week or two as I have a lovely ailment called trigger finger which is making typing rather awkward. So in lieu of a detailed blog I simply have to make a brief comment on one of the articles in this months issue

The article in which I am interested is a nice primer on mutational meltdown in mammalian mitochondrial genomes by Dave Rand. This is in relation to a paper by Stewart et al. in this issue. But enough about science. For those who do not know, Dave Rand published what I believe was the first rap in a scientific article. In an article in Genetics he presented a rap about repeat induced point mutation (something known as RIPPING). This RAP about RIPPING I think was presented at the Evolution meeting in Berkeley (I think I was at the talk where he did the RAP but I am not sure — I could have, like Andy Pettite, misremembered the whole thing).

And well, here it is:

Yo! you’ve got my DNA and you think it is a-RIPping,
Your dog is so excited her saliva is a-dripping,
She seems to think the polymerase is doing some a-skipping,
But then again, you never know, she might just be a-quipping.
Are you sure induction by repeats did make it happen?
If it’s just associated, why not call it RAPpin’?
What motifs are necessary to keep the strands a-snappin’?
I don’t know and I don’t care, but something did some zappin’.

A really good day at work

Overall, I like being a scientist. But some of the days can be quite dreary. As a grad. student you slog through days that resemble the reliving of events in Groundhog Day. Except that they are actually different days – they just seem the same. As a post doc you struggle to get work done to then get a job (OK, I skipped a post doc, but I heard about what it is like from others). And as a faculty member you spend an absurd amount of time wasted on useless administrative activities. And I sometimes seem to be stuck in these days a lot.

But today was a really good day. It was my first day after it was announced that I was the new Academic Editor in Chief of PLoS Biology. And I got lots of positive feedback from friends, colleagues and even strangers. And then we had “lab meeting” which I decided to turn into a picnic/hike. We went to a little spot only 2 miles from the UC Davis Genome Center, that was as close to wilderness as you can find in Davis. And I think everyone had fun, getting away from the grind AND I brought my 3 year old daughter too.

And this reminds me to say – in the past I have avoided talking about people in my lab in my blog because it seemed like it would be nice to give them some space from my blabbing. But today I was reminded of just how much I owe them. They of course do all the work that I end up getting credit for. So today I thank the current lab members specifically (Jenna Morgan, Amber Hartman, Marcel Huntemann, Dongying Wu, Martin Wu, and Sourav Chatterji) and with their permission you will probably be hearing more about them later.

PLoS Biology 2.0

PLoS Biology - www.plosbiology.org

Well, I guess it is official now so I should post about it here. As for this afternoon, I am now the new Academic Editor in Chief of PLoS Biology. To read more about this new role of mine go to the source. I will probably cross post the editorial here at some later point.

Also see other blogs/notes about this

For more on what I think about Open Access publishing see some of my other blogs on the issue.

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