UC Davis Bodega Marine Lab getting some props

Now, I have written here before about the spectacular site for UC Davis’ Bodega Marina Lab in Bodega Bay). And lest anyone not believe me, Bodega Bay and the Marine Lab has been written up in the San Francisco Chronicle in an article entitled: Marine lab a spectacular spot on Bodega Bay.

The article lead in is all you really need to know:

Mention Bodega Bay, and the first thing that comes to mind – even now, 45 years later – is Tippi Hedren getting her head pecked by a gaggle of sociopathic seagulls. The town’s visitor center hands out 8,000 maps a year pinpointing where Alfred Hitchcock filmed the most memorable scenes of the 1963 classic “The Birds.”

But each year, 10,000 to 12,000 people travel to a spectacular spot west of town to visit a less-famous site, the Bodega Marine Laboratory, a UC Davis outpost where about 100 graduate students and scientists study underwater life along the Northern California coast.

Each Friday afternoon, from 2 to 4, docents lead free, hourlong tours that wind through parts of the sprawling complex. It soon becomes clear that visiting a marine lab isn’t anything like visiting for-profit aquariums, with their polished tanks and fancy signs. Here, the only live exhibits are a tide pool and three small aquariums.

Mind you, Bodega Bay itself is not the most happening town in the world. But it has a few stores, restaurants and cafes (which they review some of in the Chronicle article). The lab is also the site for the “Workshop in Applied Phylogenetics.” One cool thing about this workshop is that the organizers have begun building a Wiki to gather information on phylogenetic methods and tools and this wiki is open to everyone to use and contribute to. So if you are interested in phylogenetics you might want to check out the wiki and start adding to it. And you might want to keep an eye out for announcements for next years course.

Wanna help run a major University – apply for this job

U. C. Davis, where I am a faculty, is recruiting nominations and applications for “PROVOST AND EXECUTIVE VICE CHANCELLOR.” So if you are itching for something new out there, and think you have what it takes, consider applying.

Oh, and hopefully, from my point of view, you will be more supportive of Open Access publishing than our interim Provost and Executive Vice Chancellor, Barbara Horwitz (see here and here for more on her position on Open Access).

Let me state first, that I realize that Open Access is not the only important thing in the world and that there are many kinds of OA and furthermore that some people may generally support OA but may be worried about how to get there (e.g., see Timo Hannay’s discussion of some of his concerns about doing full OA here ).

And Dr. Horwitz has done some quite good things in other aspects of her job. But her more recent foray into the OA debate was so icky, so misleading, that I am really hoping she does not become full time provost and furthermore that whomever does has a different take on the whole thing.

What was it that raised my ire? Well, she was directly involved in what could be considered a bit of a test run of the ideas behind PRISM, the much panned “coalition” against open access. I wrote about the PRISM-esque test run by Horwitz and colleagues here. In summary, she and a group of other anti-OA advocates wrote a letter stating their PRISM-esque objections to the OA movement. For example here is one of their PRISM-esque quotes

“The free posting of unedited author manuscripts by government agencies threatens the integrity of the scientific record, potentially undermines the publisher peer review process, and is not a smart use of funds that could be better used for research.”

Ooh you say — a letter — what’s the big deal. Well, the ten people who wrote the letter wrote it as individuals, but then a PRISM-esque anti OA group wrote a press release wherein they referred to the people who wrote the letters as “University Officials” which they were (all were deans, provosts, etc) and how University Officials were against OA. This was clearly done to give the impression that the Universities themselves were against OA, which was not true. And this misleading presentation was clearly done in collaboration with the letter writers. So Horwitz and crowd allowed the fact that they were University officials to be used to mislead people into thinking that their opinions were POSITIONS of the university.

Horwitz is welcome to her opinions and I agree with Timo Hannay that we need a fair and measured debate about OA (although I think he goes overboard in dinging people for being a bit agressive in their blog commentaries about it — this is after all what makes blogs a bit fun). But let’s not abuse our positions of authority and responsibility within the University to mislead about our positions. And just because we have a pleasant debate does not mean I will support an anti OA advocate to help run UC Davis, not that I have much say in the matter.

But given that U. C. Davis is strong and getting stronger in the sciences means that one key aspect of the recruitment of a new Provost and Executive Vice Chancellor should be how they stand on scientific publishing.

An innoculated mind

Here’s a somewhat self serving recommendation for people to check out the blog of Karl Mogel. He is a Davisite (who used to write for the U. C. Davis student paper) who has a radio show on Science and he has lots of interesting stuff in his blog about evolution. So check it out. Oh, and he put his interview of me online … haven’t listened yet but it can be found here.

Shameless Self Promotion

OK. I know I am not supposed to do this. But hey, are there really any rules for blogs?

I got my first major local press story since moving to Davis yesterday. The Sacramento News and Review ran a cover story on the U. C. Davis Genome Center, featuring me, Katie Pollard, and the director of the center Richard Michelmore. I of course do not recall saying any of the things that I am quoted saying but I certainly recall saying things close to what was quoted so in this case the reporter (Ralph Brave) seems to have done a fair job. I guess I would quibble a tiny bit with my portrayal in terms of the discussion of synthetic biology (I believe it is a powerful tool but that the practitioners downplay the risks).

The best part of the story – they featured my work on the glassy winged sharpshooter symbionts that we published in PLoS Biology earlier this year. That is (hopefully) good for me since the sharpshooter is a big deal out here in N. California since it is a vector for Pierce’s Disease in grapes. Plus, they were able to use a figure from my paper since of course, the paper in fully Open Access. So my work gets some extra exposure that might have been more difficult for the paper to pull off if it was published in a non Open Access journal. In essence, Open Access publishing is the gift that keeps on giving. As long as I keep getting credit for it, it is great for me that people do not have to get permission or pay a fee to use figures from my papers.

Added afterwards:

  • Egghead ran a story on this

Has your scientific research been wasted?

I had a good Thanksgiving weekend this year – spending time with family and friends. But as I go back to work this week I have now gotten somewhat depressed over something I did Sunday night. I decided to remove myself from the UC Davis internet proxy to see how many of my past papers that I have published I can obtain without the UC subscriptions. So I went to pubmed, and typed in my name (Eisen JA) and got most of my papers, which are listed at the bottom of this blog (some do not come up due to publication off the pubmed grid or due to co-authors screwing up my initials). (NOTE  – LISTING DELETED 4/09 BECAUSE THE FORMATTING IS ALL MESSED UP)

And then I went to see how many of my papers were freely available and how many were not. What I was most interested in was – what is the deal with papers I wrote before becoming an Open Access convert? For many it is easy to figure out if they are freely available – Pubmed has a link saying “Free in PMC” which refers to Pubmed Central. For others, it was a little trickier.

The results were both good and bad and a summary is below. A few things struck me. First, a lot of my life’s work is not readily available without paying other for it. In the day and age of the internet, this means that these papers will simply be read less and less as time goes by. And that makes me very sad. If I had chosen to publish those papers in other journals, anyone in the world could get them at any time. Thankfully I did publish many papers in journals like PNAS, and ASM journals, and NAR – journals that have now decided to release them to Pubmed Central. And also thankfully (but less so) I published some papers in journals that have at least made them freely available on their web sites.

Most surprisingly to me is that a reasonable number of my papers in Nature are freely available on the Nature web site as part of their Genomics Gateway program. Nature deserves serious kudos for doing this and they stand out compared to Elsevier journals (which do not seem to ever do this) and even Science. This is disappointing as Science is published by a scientific society but apparently does not seem to care much about access to publications. Nature, a commercial publisher, is in my opinion doing more for scientific openness than Science. Now, Nature has a long way to go, but I am SO glad I listened to their editors like Chris Gunter and Tanguy Chouard who made a big deal about the Genome papers being free. I did not think it was that big a deal, but in retrospect they were ahead of me in thinking about availability. Plus Nature clearly makes more of an effort to provide free online material than they have to – and certainly make more available than Science.

So in the end – I am sad about my partially wasted past. But I am pleasantly surprised that at least some papers I thought would be more restricted are actually free (although only on the Publishers site for now – Hopefully these journals will submit them to PMC at some point). I guess – you win some and you lose some and some are somewhere in between.

Summary of openness — other scientists should do this exercise

In Pubmed Central and Open Access

Available free on publisher’s sites (notideal but better than nothing)

Must buy paper

Not available anywhere

UC Davis Research Blog

Well, U. C. Davis (where I work) shows that it is both hip and dedicated to Science research with a new “Research Blog” put out by its University Communications office. It is called Egghead and its goal is:

Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

I am not sure how many other Universities have an officially sanctioned blog from the press office, but I could not find any.

My favorite post at Egghead so far is the one about a website called Adopt a Microbe. There is
absolutely no Davis connection to this site yet the wrote a tiny blurb about it anyway. I hope they continue to do things like this – it can get tedious if the blog is all about promoting Davis research only. It will certainly get read more if there is a diversity of stuff there.

It is good to see that Biology is the top subject there … not that there is anything wrong with other fields but one of the reasons I wanted to move to U. C. Davis was because of the amazing diversity of biology-related research going on on campus.

Now if they could only get a weekly podcast going …

If anyone out there knows of other Universities with interesting Blogs from the press office, let me know.

Moving to Davis

Well, it has been a while. Things got a little out of hand in life. I am now a Professor at U. C. Davis, in their new Genome Center.

Prior to Davis, I was at The Institute for Genomic Research (TIGR), an incredible place that pioneered genome squencing and analysis. I was a faculty there from 1998-2006 and felt like a kid in a candy shop pretty much the whole time there.