Tag: Misc.

Happy Birthday Anna Eisen 8-8-8 at 8:08 PM

Happy Birthday Anna Eisen (my niece)

8/8/08 at 8:08 PM

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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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New Yorker on Superbugs

Still catching up after being out sick with an antibiotic resistant infection. But I had to post on this one. The New Yorker has new piece by Jerome Groopman on, well, antibiotic resistant bacteria. See Medical Dispatch: Superbugs: Reporting & Essays: The New Yorker

Thanks to Saul J for pointing this out.

I particularly like the ending

No one, Moellering said, has developed a way to disarm bacteria sufficiently to allow the human body to naturally and consistently defend against them. I asked him what we should do to combat these new superbugs. “Nobody has the answer right now,” he said. “The fact of the matter is that we have found all the easy targets” for drug development. He went on, “So the only other thing we can do is continue to work on antibiotic stewardship.” Meanwhile, new resistant bacteria, Moellering asserted, aren’t going to go away. “We can temper things, we might be able to slow the rate of emergence of resistance, but it’s unlikely that we will ever be able to conquer it.”

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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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Best time to appreciate Open Access? When you’re really sick and want to learn more about what you have.

Well, I have been out sick for a while. But I am now finally apparently getting better. Thanks to the work of scientists who have developed multiple classes of antibiotics. Anyway, more on that later. While I was out sick I spent a lot of time searching the web for information about nasty, cellulitis causing antibiotic resistant bacterial infections. And I was researching some other health related issues that may have contributed to my getting such an infection. Here are some tidbits I learned during this forced homecation.

  • Complete OA still a long way off. One thing I re-learned during this was that it is incredibly frustrating to see how much of the biomedical literature is still not freely available online. Shame on Elsevier and all the others who are still hoarding this important information.
  • Thanks to those providing OA. Related to the above issue, I came to appreciate was the societies and publishers have decided to go the OA route. I spent a lot of time reading material from ASM, BMC, PLoS, Hindawi, and a few others. And I am grateful to these groups.
  • Google rocks for science searching. Cuil, not so much. If you need to find something about some scientific concept or issue, Google really does a great job. While I was out, Cuil was announced as a possible new competitor for Google in searching. From my experience, Cuil is really really lame for science searches. I like their presentation in a magazine style. But the search results were not so good.
Anyway, enough about me. This is just a quick post to say the Tree of Life will be coming back over the next week or two. I am still out sick. But a clear sign to me that I am getting better is that I finally want to blog again.
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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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Staying clean

Well, sorry for the lack of posting recently. Out sick thanks to a fun antibiotic resistant bacteria. In honor of that here are some tips to staying clean:

A Germ-Zapper’s Guide to Clean (from the Washington Post

hat tip to Doug Rusch for pointing this out and giving me something to do other than worry about bacterial infections)

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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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Is your city walkable?

Just got an announcement from a friend of mine who has started a new campaign for trying to “raise America’s Walk Score.” They have launched a web site www.walkscore.com with walkability rankings of 2,508 neighborhoods in the largest 40 U.S. cities. If you go to the site and type in your address you can see how you score (Downtown Davis does really well). And if you support walkable communities they have a petition online to encourage Congress to support walking towns …

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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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Closed Access Award #1: American Psychological Association

Well, I wrote up this award a short time ago and already the story has changed. But I am still giving the award. On Tuesday, Peter Suber reported that

The American Psychological Association may have the worst publisher policy to date for NIH-funded authors. Excerpt:

In compliance with [the NIH OA policy], APA will deposit the final peer-reviewed manuscript of NIH-funded research to PMC upon acceptance for publication. The deposit fee of $2,500 per manuscript for 2008 will be billed to the author’s university per NIH policy….

Even after collecting the fee, the APA will not deposit the published version of the article, will not allow OA release for 12 months, will not allow authors to deposit in PMC themselves (and bypass the fee), will not allow authors to deposit in any other OA repository, and will not allow authors to retain copyright.

I agree with Peter that this is a stunningly inane move on their part (for more discussion see Suber’s follow up here). They are basically saying that to carry out a simply electronic submission they will charge $2500.

Apparently someone convinced them this was not the brightest thing in the world to do as they are now reconsidering this move (I learned about this reconsideration from the Scientist magazine blog here … you need to register to read the blog). This blog reports

A statement sent to The Scientist today from APA Publisher Gary VandenBos said: “A new document deposit policy…is currently being re-examined and will not be implemented at this time…APA will soon be releasing more detailed information about the complex issues involved in the implementation of the new NIH Public Access Policy.”

VandenBos was not available for further comment.

Even though they are reconsidering their policy, since they have not out and out rescinded it, I am still giving the American Psychological Association my first “Closed Access Award” for this incredibly silly move

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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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Stanford – Promoting open access while selling access to "closed" journals

Some people may have seen the press Stanford got a few weeks ago regarding the Open Access initiative of their School of Education. For some more information on this see

  • Stanford’s Education School Requires Open Access

  • Stanford University School of Education’s Open Access Mandate—Harvard Medical School Next?

  • Science Commons » Blog Archive » A new open access mandate at Stanford

    • Certainly sounds like a good move on their part. And then I got an interesting thing in the mail from the Stanford Alumni Association (I earned my PhD from Stanford) trying to get me to join the association (see letter below). What was the selling point? If I joined I would get access to newspapers, periodicals and even scientific journals, through their library. So Stanford is all for OA in some places. But while they have access to closed journals, they will use that as a recruitment tool to join the Alumni Association. Seems to me like a better way to push for Open Access would be for all of Stanford to take the School of Education’s position and for the university to immediately cancel all subscriptions to completely closed access journals.

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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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    Saving Money and Gas and the Planet by Not Travelling

    A UC Davis professor has been getting some local press for NOT going to a meeting . Well, OK that is not exactly the point. He (Timothy Morton) gave his talk remotely by video taping it and then having the people in Scotland watch the DVD and then talk to him.  The reason for the news coverage is that by doing this this saves both money and carbon output.  Given that I have been canceling trips left and right recently for some medical reasons, I like this idea.  

    I even gave a talk over iChat to a metagenomics gathering in Berlin that was organized by Dan Falush.   I was supposed to go to to this workshop last week as a run up for the International Congress of Genetics (which I have also bailed on but they did not offer to let me speak remotely).  
    I might add that doing a talk by iChat worked out OK … we probably needed speakers for the computer on the other end and microphones so I could hear the discussion.  And not sure my talk was any good.  But technically, iChat worked out fine.

    So what I am now going to say is that I am canceling the trips for environmental reasons …

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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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    Wanted -Microbial Genomics Lead at JGI

    The Joint Genome Institute, where I work part of the time, is seeking a lead scientist for their Microbial Genomics work.

    Sr. Research and Management Opportunity

    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting Staff Scientist opportunity available. Will be responsible for leading the JGI’s Microbial Genome Program including the development of an independent research program in microbial genomics. Will manage all aspects of the program from application review through sequencing and genome analysis. Will be expected to collaborate with external scientific communities, present scientific data and publish results independently and with collaborators. Will also participate as a member of the JGI senior management team. This position reports to the Deputy Director of Scientific Programs.

    For more information see here. If you want to play a leadership role in microbial genomics, this job is for you.
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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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    How will I survive? iPhone Upgrade crashed …


    Well, not my normal posting here. But I have been trying to use my iPhone more and more for blogging and was excited about some of the new software upgrades that were made available today. And so I started the upgrade. And the iTunes server has apparently crashed and now my phone is stuck in “Emergency calls only” mode. So much for mobile blogging for today at least.

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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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