Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

GIS mapping of bike accidents in Davis

A PhD student in my lab has generated a nice GIS mapping of auto and bike accidents in Davis, CA.  Worth browsing …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Swine Flu Hits Davis?

Seems like Swine Flu (aka H1N1) has hit Davis.  See here. 

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Swine Flu Hits Davis?

Seems like Swine Flu (aka H1N1) has hit Davis.  See here. 

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Access Pioneer Award: Rick Prelinger, Image Access

Just saw an interesting article in the UC Davis “Dateline” newsletter about Rick Prelinger who is the founder of the Prelinger Library in San Francisco (and see their blog here). He gave a talk at Davis and thus they wrote an article about him here.

Some good lines from the article include

Rick Prelinger’s biggest thrill is “mainstreaming” historical documents for public consumption.

But getting history into the hands of the average citizen is no easy task, the archivist says.

Overbearing copyright issues and rampant commercialism, he argues, threaten the free exchange of information on which a knowledge society — especially its libraries — depends.

…

Rather than concern themselves with rigid lending policies or copyright protections, library systems should focus on “more product, less process” to better serve patrons, Prelinger said.

…

“If the Google book deal is approved without any changes, we could soon lose 100 million books that society doesn’t know what to do with,” said Prelinger, referring to “orphan works,” or works under copyright, but whose owner is not known.

….

On the other hand, archives are empowering, Prelinger said. “Let’s open up the past. Interesting things happen when we do so.”

In general since Prelinger has been pushing for more openness in libraries and in images, I am giving him an “Open Access Pioneer Award“.  Sorry I missed the talk but glad I read the article.  

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Flu: Up to date Open analysis of Human/Swine A/H1N1 Influenza

Just got a pointer to a fantastic site with detailed up to date analyses of flu (e.g., swine flu) data. The site is http://tree.bio.ed.ac.uk/groups/influenza/. The site says

These pages are to allow the rapid dissemination of results and analysis of genetic data from the ongoing Influenza A/H1N1 outbreak attributed to swine flu.

And there is some great stuff there posted by among others, Andrew Rambaut, Oliver Pybus, Nicholas Grassly, Mike Worobey and Gavin Smith. Definitely worth checking out. Hat tip to Eddy Holmes for pointing this out.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Marketplace piece on open access

Marketplace on NPR had a mini story on Open Access publishing. See Marketplace: Publicly funded research for a price. Hat tip to Aaron Gussman and Keith Bradnam for pointing this out. I did not listen to the piece but the text is online here. Here are some bits (does not seem to be a particularly well researched piece but it is still something)

KAI RYSSDAL: A lot of the scientific research that goes on in this country is really expensive. And, as it happens, a lot of it is publicly funded. But when taxpayers want to read a particular study that has been paid for with their money, they have to pay again to read about it in, say, The New England Journal of Medicine.
…

JANET BABIN: People who grew up with the Internet expect information to be free. That’s what 21-year-old Josh Sommer thought. In 2006 he was a typical college freshman. Studying environmental engineering, hanging out, making new friends. Suddenly, he started to get severe headaches. He had a series of routine tests.

JOSH SOMMER: End up having an MRI and being told that I have a mass right in the very center of my head, entwined with critical arteries, in one of the most difficult locations to operate on. The cancer Josh has is called Chordoma. It’s a rare disease with a low survival rate. Even doctors don’t know much about it. So Josh threw himself into Chordoma research. He Googled the disease to find out all he could about it, but kept hitting roadblocks.

SOMMER: I’d find an abstract, and I’d click on it. And oh, you have to pay $60 to read this article. Oh, you have to pay $40 to read this article. I mean, I have this disease, I want to know about it. Journal subscriptions — like the Journal of the American Medical Association — can cost thousands of dollars each year. With universities and libraries trimming budgets, they can’t afford all of them either. What Josh needed was free access to the research online. Last year, the National Institutes of Health unlocked the gates on a lot of research. Through its Web portal called PubMed Central, you can now search research papers for any disease scientists are studying with public funds. It’s an estimated 80,000 articles a year. Duke University law professor James Boyle says open access is only fair.

JAMES BOYLE: Why would you possibly say that when the taxpayers funded something, then the public can’t get to read it afterwards without paying again?

…
Then they quote Martin Frank from the American Physiological Society. saying something defending restricted access. They also quote rebuttal from Professor Boyle, at Duke:

BOYLE: The Web works great for porn or for shoes, or for flirting on social networks. But it doesn’t work really well for science. We haven’t done for science what we did on the rest of the Web, which is basically to have this open Web with everything linked together.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Assembling the Marine Metagenome, One Cell at a Time

As I have already divulged on twitter and friendfeed, a paper on which I am an author just came out in PLoS One. The paper is Assembling the Marine Metagenome, One Cell at a Time

It represents a collaboration between a bunch of different institutes including the Joint Genome Institute, UC Davis, and the Bigelow Lab in Maine. The main thing in the paper is the use of whole genome amplification to aid in the sequencing of the genome from a single cell.

The first author on the paper Tonja Woyke at the Joint Genome Institute has been adopting and developing methods for this type of single cell work (extending for example the MDA “multiple displacement amplification” protocol. Woyke is one of those rare types who can do both complex lab work and genome analysis and a variety of other things and is also great to be around.

The other main player in the project was Ramunas Stepanauskas from the Bigelow Lab in Maine who is the “biologists” with an interest in the specific samples which were being worked on. These samples were flavobacteria (a type of bacteria) that live in surface ocean waters but have never been grown in isolation in the laboratory. And in such cases, single cell genomics is very useful and powerful. In the paper we show that having this genome is quite useful for interpreting metagenomic data (not surprising, but good to show).

Anyway – check out the paper if you are interested in microbial ecology and/or metagenomics. Or look at the press release here.


Figure 2. Biogeography of microorganisms closely related to MS024-2A and MS024-3C.
A. Geographic distribution of the Global Ocean Sampling (GOS) metagenome fragments with >95% identity to MS024-2A and MS024-3C DNA. Numerals on the map indicate GOS station numbers. B. Sea surface temperature in December 2003, which demonstrates hydrological separation of GOS aquatic samples collected north and south of Cape Hatteras (near GOS station 13). Provided is a composite Aqua-MODIS image for December 2003 (http://oceancolor.gsfc.nasa.gov). The GOS stations were numbered in the order of their sampling, and stations 12, 13 and 14 were sampled on December 18, 19 and 20, 2003.
doi:10.1371/journal.pone.0005299.g002

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Access Flu – Updated

In regard to the swine flu infections going on, here are some Open Access PLoS papers articles about flu.  In total they provide some useful background reading on flu that anyone can get access to.  I have updated the list after prodding from @bpb on Twitter …

More from PLoS Pathogens (click here for a link to a title search for “influenza”)
More from PLoS Medicine
More from PLoS Computational Biology
More from PLoS One (see even more here)
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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A blog posting of my email signature to reduce clutter.

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Jonathan A. Eisen, Ph.D
With appointments in:      UC Davis Genome Center
Academic Editor in Chief, PLoS Biology

Mailing address:
UC Davis Genome Center
451 East Health Sciences Drive
Davis, CA 95616-8816

Blog: http://phylogenomics.blogspot.com/
Twitter: http://twitter.com/phylogenomics/
FriendFeed: http://friendfeed.com/treeoflife/
LinkedIn: http://www.linkedin.com/in/jonathaneisen
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Support open access to scientific literature:http://www.publiclibraryofscience.org

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In order to reduce the length of my signature in my email, I am posting my signature here and then am tinyurling the link in order to make it as short as possible and not clutter up my email (so now my signature reads http://tinyurl.com/jonathaneisen). I do not know if anyone else does this or if there is a better way to do it I would love to know. I have deleted the phone # and email address portions of this but it does have most else.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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The dope on brain doping take 2

The New Yorker has a long article on Brain Doping (or as others like to call it, cognitive enhancement) by Margaret Talbot. I was interviewed for it a while ago because of my mischevious April 1, 2008 blog/web joke I coordinated announcing that NIH was cracking down on brain doping.

And although they do not mention my April 1 joke in the New Yorker article, they do quote me

Still, even if you acknowledge that cosmetic neurology is here to stay, there is something dispiriting about the way the drugs are used—the kind of aspirations they open up, or don’t. Jonathan Eisen, an evolutionary biologist at U.C. Davis, is skeptical of what he mockingly calls “brain doping.” During a recent conversation, he spoke about colleagues who take neuroenhancers in order to grind out grant proposals. “It’s weird to me that people are taking these drugs to write grants,” he said. “I mean, if you came up with some really interesting paper that was spurred by taking some really interesting drug—magic mushrooms or something—that would make more sense to me. In the end, you’re only as good as the ideas you’ve come up with.”

I am sure the quote is reasonably accurate. However, it does not include the whole discussion behind the quote. What I said was that staying up all night while on ritalin to write a grant proposal seems silly (and after my Arpil 1 joke was outed, multiple people told me they actually do this). What you need to get a grant funded is good ideas and these do not seem to come from just popping some drug to keep you mind clear when you should be sleeping. So I said something like taking a drug to help give you new ideas – that could make sense (and thus my reference to shrooms which I have by the way never done). Because if that helped you devise some cool new things to do – that it what people look for in grant proposals. Elegant text about something boring – who cares. Not that the writing part of a grant is unimportant but I still do not see how most of these brain doping drugs would help with doing something interesting in science. Ideas without good text – unlikely to get a grant but possible. Good text without a good idea – I would hope no grant would be awarded.

But the quote does make me sound like I am encouraging hallucionagens, which was not the point … oh well. In this case, no criticism of the New Yorker – just wish they had included a bit more about why I said what I apparently said … I guess next time I should just say “Ideas are the key. Not churning out bad text at the last minute”

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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