Eisen Lab Blog

Just went to Pubmed and saw a link to a new service at NCBI called Rapid Research Notes (Rapid Research Notes)

Seems like right now all that is there is PLoS Currents (not that that is a bad thing — I love PLoS Currents). Apparently more will be coming. From their website:

About Rapid Research Notes

The National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at NIH, is a national resource for molecular biology information and as such has a mandate to develop new products and services to meet the needs of the biomedical research community. Upon the recommendation of public advisors, NCBI developed an archival service to support research shared through new venues for rapid communication enabled by the internet. Introduced in August 2009, the archive, called Rapid Research Notes (RRN), allows users to access and cite research that is provided through participating publisher programs designed for immediate communication.

The RRN archive was prompted in part by the spring 2009 worldwide outbreak of H1N1 influenza and the call for a means to quickly share research information about this critical and emergent public health threat. To address the influenza information sharing need, the Public Library of Science developed PLoS Currents: Influenza, the first collection being archived in RRN. NCBI expects the RRN archive to expand over time to include additional collections in other biomedical fields and other critical topics.

Publishers interested in archiving online, rapid communications in RRN should contact NCBI at RRN@ncbi.nlm.nih.gov. General guidelines for participation are described below; these guidelines are provisional and may change as NCBI gains experience with the new RRN archive.

The world of publishing is changing. With things like PLoS One, PLoS Currents, RRN, Nature Precedings, etc. and more coming. Time to buckle up and get ready for a good ride.

Congrats to #PLOS One and everyone behind it for winning the Association of Learning and Professional Society Publishing (ALPSP) Award for Publishing Innovation.

PLoS ONE Wins ALPSP Award for Publishing Innovation 2009 – “bold and successful and shaping the future of publishing” everyONE – the PLoS ONE community blog

I personally really really really like the PLoS One publishing model. PLoS One reviews papers based on technical merit (that is a paper has to be scientifically and technically sound). But it does not review papers based upon reviewers notions of “importance” or “interest” or “relevance”. Instead, the goal is to let that evaluation happen after publishing.

This simple shift in publishing, which has been attempted a few times previously in various biomedical publications, is revolutionary. To go with this new approach to pbulsihing, PLoS One is working to encourage after publication commening and evaluation of papers. I simply love this model and think it is a great idea (I had nothing to do with the planning of PLoS One, so am not tooting my own horn here). I confess I did not completely get the concept behind PLoS One at first, but now I get it. And I embrace it. Consider my four most recent papers in Pubmed – three are in PLoS One (and one is in PLoS Genetics):

1. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).
2. Assembling the marine metagenome, one cell at a time.
3. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.

I really do like PLoS One.

Ghostwriting is much more prevalent in medical publications than many appreciate according to a new study discussed in the New York Times (Ghostwriting Widespread in Medical Journals, Study Says)

The exact details of this new study are unclear, since it is not published, but basically, a survey of authors reveals (among those responded) a remarkably high rate of “ghostwriting” where someone not on the author list made major contributions to the writing of papers.

As I have said before – openness is a way around this — but of course only if everyone is honest. What people did as part of a paper should be reported in as much detail as allowed. Who did experiments? Who did analysis? Who did writing? Etc etc etc. It should all be stated somewhere. And many journals are moving in this direction. But alas, apparently people are not revealing all the details. Not sure what the solution to this problem is – but I can’t help but think that we need to revamp the general discussion of authorship ethics within the scientific community —

Dear Colleagues,

I just got this email. Not sure how I feel about this (I disagree with some of the statements here but sympathize with the feelings of many of the faculty)(UPDATE – I think this whole boycott/walkout concept is unclear and strange and will not participate in it — ) but thought I would post it for people interested.

As you may have heard, there is a broad movement to defend the future of public education in California, to restore faculty’s role in shared governance, and to protect the most vulnerable employees within the UC system. It has become increasingly clear that these goals require an immediate and firm rejection of the manner in which the administration has handled the budget crisis over the summer. Last week, a systemwide call went out for faculty to take action on September 24.

You can see and support this call, as of this morning, at ucfacultywalkout.com

With limited circulation, this call has already been signed by hundreds of faculty in the UC system.

• It has been fully endorsed by the National AAUP.
• In coordination with this action, UPTE — an employee-run union with 12,000 members in the UC system — has called a strike and picket on 9/24
• The Solidarity Alliance at UCBerkeley has called for a “Walk-Out and Teach-In” on 9/24
• Option 4 at UCSB has declared “A Day of Learning, Solidarity, and Protest on 9/24”
• Saving UCLA has called for “A Day of Action” on 9/24
• The Graduate Student Union Organizing Committee at UCB is distributing an open letter calling for all UC GSIs to honor picket lines on 9/24, as they are contractually entitled to do.

These are some examples of the efforts already well under way to stand in solidarity with students and staff in defense of public education.

The call for the 9/24 actions, available at the website, calls for three demands on behalf of the future of public education in California. These demands are meant to insist upon:

1) Protection for the most vulnerable employees in the UC system
2) Respect for democratic process of decision-making
3) Information for public access concerning the handling of the budget cuts

If you support these basic goals as necessities for the University to pursue its educational mission, please sign on to the call at

ucfacultywalkout.com

If you would like further information on a simple, easy-to-organize action and education plan authored by UC faculty, we’re able to provide this. Just ask.

With thanks and admiration for your commitment to the UC system and its future,

UC Faculty Walkout organizers

Nice little article by Carl Zimmer in the New York Times today: Where Did All the Flowers Come From? – NYTimes.com

The article discusses flower evolution and has some good points. One in particular comes from Jim Doyle from UC Davis, who points out that one needs the fossil record to understand the evolutionary emergence of fossils flowers. It is a good thing to remember for all the gene jockeys (like me) out there who sometimes seem to think everything can be figured out from DNA.

Stay tuned for more about this in my blog – I am teaching a 750 person class “Bis 002C – Biodiversity and the tree of life” with Doyle and Peter Wainwright this fall and will be posting some notes based on the class. Maybe Doyle will make some other key points there …

The California Academy of Sciences is putting on a Bioforum for science teachers on:

Genomics: Insights and Impacts
Saturday, October, 3, 2009
9:00 am – 3:00 pm

Talks will be by me, Katie Pollard, Jeffrey Boore, and Nadav Ahituv

From their website one can get more detail on the Bioforum:

BioForum is a twice-annual seminar series for middle school and high school science teachers. Each symposium is held at the California Academy of Sciences and features presentations on current science and sustainability topics by renowned researchers. The presentations are followed by a panel discussion and question-and-answer session with the speakers and the moderator. BioForums are excellent professional development opportunities for science educators, providing up-to-date information on research that will enrich their teaching.

For more information see: Teachers: California Academy of Sciences

Just got this announcement. The Gates Foundation has been funding some really cool stuff … if you work on any of these topics it is probably worth thinking about putting in an Application

The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 4 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions. Anyone can apply, regardless of education or experience level.

Grant proposals are being accepted online at http://www.grandchallenges.org/explorations until November 2nd 2009, on the following topics:

New! Create New Technologies for Contraception
Create New Ways to Protect Against Infectious Disease
Create New Ways to Induce and Measure Mucosal Immunity
Create Low-Cost Diagnostics for Priority Global Health Conditions

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the new topics and application instructions are available at http://www.grandchallenges.org/explorations.

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you don’t submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world’s greatest health challenges.

What should be the next genome sequenced? Olivia Judson has turned this question into an analog of Fantasy Baseball. Submit your suggestions to her/the world at The Fantasy Genome Project – Olivia Judson Blog – NYTimes.com

Or submit them here. For microbes it is so cheap that there is no point in doing this type of competition (e.g., for a bacterial isolate it would cost ~ 1-2000$$$ to do the shotgun sequencing for most species and then if you want to finish it would cost more, but still not very much)

My suggestion for a bigger genome to do that would be fun, interesting and important — the blue whale. Biggest animal on the planet. Ever. Just must have its genome.

PLoS Currents is live (as of last week). Check out the blog posting by Harold Varmus:A new website for the rapid sharing of influenza research | Public Library of Science

I am very excited by this — it seems to be a new step on Open Science.