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

Some outdated webpages of mine need external links

Here are some links to some very outdated webpages of mine.  I want them to come up in Google Searches and this seemed the best way.  I am back posting this a year to hide it from the front of my blog.

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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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Shameless Self Promotion # 200: Are We Alone

Just a little quick link here. People might be interested to check out the “Are we alone” Radio Show from July 21, 2008 (Are We Alone). A direct MP3 link is here. Here is there summary of the show from that date:

Remember Mr. Potato Head? You changed his look by snapping in plastic mustaches, googly eyes and feet. Now imagine doing the same with a living cell: inserting the genes you want to create the organism you want. Welcome to the world of synthetic biology. It has potential to create new bio-fuels and life-saving drugs. It also ushers in a host of ethical and safety concerns. We examine both when we discuss this emerging science of mix and match genes. Plus, does doing an end run around Mother Nature challenge the essence of life itself?

Guests:

This show is produced by the SETI institute and has some interesting topics on different science things.

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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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Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC)

SPARC has a nice set of talks online about Harvard’s move towards a University wide open access system (see Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC))

From the web site
“This spring, Harvard’s Faculty of Arts and Sciences voted to enable open access to their scholarly articles in an institutional repository. This vote granted the university the rights necessary to archive and make freely available on the Internet articles written by Arts and Sciences faculty members. It is the first time the faculty of a U.S. university has voted for an open access directive and the first time a faculty has granted permission to the university to make its articles available through open access. It is because of this vote, and the efforts leading up to it, that the Harvard FAS was named as the SPARC Innovators for June 2008.

The forum offers an exploration of the motivations behind the Harvard policy, the groundwork invested in its creation, reactions and outcomes to date, and the broader implications of this historic step. Headlining the event is Stuart M. Shieber, professor of computer science at Harvard, director of the Center for Research on Computation and Society, faculty co-director of the Berkman Center for Internet and Society, and the key architect of the policy.

Shieber is joined by Catherine Candee, executive director, Strategic Publishing and Broadcast Initiatives, from the office of the president of the University of California, who relates similar activity in the UC system; and by Kevin L. Smith, JD, scholarly communications officer at Duke University, who suggests legal considerations for institutions following the open access policy path.”

Hat tip to Michael Rogawski from U. C. Davis for pointing this out. In particular, he and I are very interested in the discussion by Catherine Candee about why the UC system did not do this before Harvard (we are hoping to get the UC to do something like this). Rogawski has also pointed me in the direction of some nice tools for sharing my publications through the UC system (see his BE Press site 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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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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Open Metagenomics Highlight: Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

OK – it is not quite metagenomics, but there is new paper in PLoS One worth looking at if you study uncultured organisms. This paper (Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing) reports on a slightly new twist in carrying out deep rRNA surveys of uncultured microbes using one of the “next” generation sequencing methods.

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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 Metagenomics Highlight – PloS Biology paper reporting more from Banfield lab on the Acid Mine Drainage

Just a quick “Open Metagneomics” posting here. There is a very interesting paper in PLoS Biology that just came out reporting more detail from Jill Banfield’s lab on their studies of an Acid Mine Drainage (AMD) site. This paper is ostly a population genomic study of the microbes living in the AMD. See the paper at PLoS Biology – Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation.

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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 #2: Andrey Rzhetsky, Michael Seringhaus and Mark Gerstein

Just got pointed to a new paper by someone near and dear to me. In this paper (Seeking a New Biology through Text Mining), Andrey Rzhetsky, Michael Seringhaus and Mark Gerstein seem to argue for the importance of text mining for the future of biology research. Text mining is indeed an important new tool in biology. Of course, it works best if you have access to the text. Alas, I would tell you more about their paper, but I have been out sick and stuck at home, and I do not have access to their paper, which was published in Cell. And thus, even without seeing their paper, I am giving them my second “Closed Access Award” for apparently outlining a path for a new biology that will be only available to some, not all.

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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 Anthrax: Open access publications for those writing about B. anthracis

Well, I am sure there are going to be a million news stories and blogs over the next few days about the anthrax letters. That is because of the recent death of someone who appears to have been the latest suspect in the anthrax mailings (see for example CNN Report: Anthrax suspect kills self as FBI closes in). (Also see the LA Times, which broke the story). I must say, after the disastrous handling of some of the previous suspects, I think we should reserve judgement on this case until some of the evidence is made public.

In the interest of helping out some of those interested in the science of studying the organism that causes anthrax I am posting here some links to fully open access articles on B. anthracis.

PLoS One papers

PLoS biology Papers

Biomed Central 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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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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