Saturday, March 29, 2008

Metagenomics Education

Just a quick one here. I was reminded recently about an interesting publication about metagenomics education in which some people might be interested. It is by Anne Jurkowski, Ann Reid and Jay Lebov and was published in a journal called CBE Life Sciences Education. This journal, though not fully Open Access is freely available online.

I think the article is a useful callto arms for educators to get ahead of the curve and to start thinking about ways to teach metagenomics BEFORE it becomes an old field (i.e, while it is hot, and who knows how long that will last).

Wednesday, March 26, 2008

A different kind of Open Science - the need to track funding sources and conflicts of interest

Well, the News is abuzz with discussion of a controversy involving lung cancer studies that were funded by tobacco associated money (e.g., see MSNBC and TIME and the NY Times). The issue is that apparently the source of the money was hidden through some sort of laundering of the money through a foundation.

As many readers know, I am a bit obsessed with open access to scientific research publications. This here is a case where the need for openness goes well beyond publications. Here there is a need for openness about funding and conflicts of interest and the roles of all participants. In this case, I am not sure what could have been done by the journals involved to vet the funding of the project more carefully. But nevertheless, science in general can be severely hurt whenever there are cases of even the appearance of conflict of interest. I do believe that open access journals help in this in that anyone, anywhere, can look at the publication as well as the descriptions of the funding sources and the authors contributions. The more eyes we have on research products, the more likely problems will be discovered and (possibly) the less likely it will be to happen again.

Friday, March 21, 2008

Happy to get this email on NIH Policy on Enhancing Public Access to Archived Publications ....

Well, the new NIH policy is not perfect, but it is a good first step. And I must say, I got a tingle of excitement when I got this email from the UC Davis Administration:
March 20, 2008

I am writing to alert you to a new requirement for investigators who receive funding from the NIH. Under the Consolidated Appropriation Act of 2008, the NIH will require that all NIH-funded investigators submit or arrange for the submission of an electronic version of their final, peer-reviewed manuscripts accepted for publication to the National Library of Medicine’s PubMed Central. PubMed Central (PMC) is the NIH’s publicly-accessible, digital archive of full-text, peer-reviewed journal articles. This new law requires manuscripts to be made publicly available via PMC no later than 12 months after the official date of publication. Please note:

1. This requirement applies to all peer-reviewed articles that arise, in whole or in part, from direct costs funded by NIH, or from work of NIH staff, that are accepted for publication on or after April 7, 2008.

2. UC Davis investigators are responsible for ensuring that any publishing or copyright agreements concerning submitted articles fully comply with this requirement. To satisfy this obligation, UC Davis investigators should enclose a copy of the one-page letter prepared by the UC Office of the President with any articles submitted to publishers for possible publication either at the time the article is submitted or with the publication agreement. The subject letter is available at:

3. The final, peer-reviewed manuscript submitted to PMC must include all graphics and supplemental material that are associated with the article.

4. Beginning May 25, 2008, anyone submitting an application, proposal or progress report to the NIH is also required to include the PMC reference number when citing applicable articles arising from NIH-funded research. This requirement applies to proposals submitted to the NIH for the May 25, 2008 due date, as well as subsequent due dates.

5. Certain publishers have agreed to automatically submit articles to PMC on behalf of the authors. The list of these publishers can be accessed at

Even if a publisher is on this list, UC Davis investigators should verify that their published articles will be submitted to PMC in compliance with the law. If the publisher is not on the list, UC Davis investigators are responsible for submitting their articles to PMC and verifying receipt of the article.

6. Failure to comply with this policy may jeopardize future NIH funding.

Additional information about this law is available at Also, the UC Davis Library can provide further assistance to investigators. Please see or contact the Library’s sciences department heads:

Breaking News: PZ Myers expelled from Expelled (the Movie)

Everyone must read, immediately, Pharyngula now.

PZ Myers writes about how he was expelled from the movie Expelled (a pro Intelligent Design movie). And the best part - Richard Dawkins was allowed in ...

Monday, March 17, 2008

Genomes of Energy and the Environment - JGI Users Meeting

Just a little post here --- if you are interested in Metagenomics, or Bioenergy or Microbes, consider going to the JGI Users Meeting March 26-28. Speakers include at least one Nobel Laureate (Steve Chu) as well as Mitch Sogin, Jill Banfield, Terry Hazen, and many others.

Friday, March 14, 2008

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."

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

Sunday, March 09, 2008

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."

Friday, March 07, 2008

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.

Monday, March 03, 2008

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.

Sunday, March 02, 2008

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.

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