Category: Misc.

Larry Moran on Phylogenomics, my new paper, and species

Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.

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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 Open Access Day: Back to Genome Biology for Me

Well, good timing on this one. A new paper from Martin Wu in my lab has recently been accepted to Genome Biology and the provisional PDF was posted online 10/13. The paper ( A simple, fast, and accurate method of phylogenomic inference ) describes a new program Martin wrote called AMPHORA and shows how it can be used to build phylogenetic trees based on concatenated alignments of housekeeping proteins and also for metagenomic phylotyping using a diversity of protein markers. As today is Open Access Day I thought I would just put in a plug for this OA paper and thank Martin for his great work and commitment to Open Access.

I should note – I really really like Genome Biology as a journal – even though they have been rejecting many of my papers lately (or maybe in part because of this). I am really glad this one got in there. I published my first fully OA paper in Genome Biology in 2000 (on symmetric genome inversions in bacteria and archaea — a paper co-authored with Steven Salzberg, Owen White and John Heidelberg – see Evidence for symmetric chromosomal inversions around the replication origin in bacteria). It is one of my favorite papers from my entire career, as in it we report on a pattern that turns out to appear to be one of the few rules of bacterial and archaeal genome evolution. Anyway – glad to be back in Genome Biology.

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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 Day: Video of a Talk I Gave About OA

Well, I was going to write all this blather about OA. But I realized it would be easier to share a video of a talk I gave at U. Washington on Open Access as part of their Biomedical Research Integrity Series (U. Washington Program). I cannot figure out how to download/embed the video so instead I am just posting the links. If someone has software for downloading it and wants to help me embed it and/or upload to YouTube and SciVee that would be great ((NOTE – VIDEO IS NOW EMBEDDED BELOW THANKS TO FRANCOIS MICHONNEAU) . Here are the links:

Lecture #2, Responsible Authorship:

Thursday, August 7, 2008; Speaker: Jonathan Eisen, Ph.D., “Responsible Authorship and the Ownership of Scientific Knowledge: Thoughts on Open Access Publishing”
To view the lecture, click here: Flash Player version, Windows Media Player version, or QuickTime Player version (for QuickTime players you may have to open the player and paste the url: rtsp://media.depts.washington.edu/uwbri/BRI_Eisen_2008.mov)

http://www.scivee.tv/flash/embedPlayer.swf

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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 Day: Thanks to OA Journals Staff

Well, today is a big day for Open Access, as it is, well, Open Access Day. And one thing I really wanted to put out there is that I think we all should say a big thanks to all of those who have worked tirelessly at various OA journals to help move OA into the mainstream and to produce a vast collection of fully open biomedical and scientific literature.

As I am involved in PLoS journals in many ways, I want to thank all of the staff who work behind (and sometimes in front) of the scenes there. There is a relatively full list of these people here. And I am publishing that list here too, with, along with a heartfelt thank you. Thank you. You all rock. And we should also thank all the staff at other OA Publishers (e.g., BMC). You rock too.

PLoS Staff

Finance/Administration Team

Strategic Alliances/Development

IT/Web Team

Publishing Teams

Marketing Team

Production Team

PLoS Biology Team

PLoS Medicine Team

PLoS Community Journals Team

PLoS ONE Team

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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 Day

Today is Open Access Day.  For more information see here.  It is a big celebration of, well, Open Access to scientific and medical literature.

We are going to have a little shindig at Davis (organized by a grad. student Collin Ellis who is also starting a new organization here on Campus – the UCD-SSOA (Society of Scientists for Open Access).  The shindig will include a live WebCast of OA Day presentations by Richard Roberts (who has one of them Nobel Prize thingies) and Phil Bourne (Editor in Chief of PLoS Computational Biology, and creative mind behind a ton of OA initiatives).  The meeting will be in the Genome Center, GBSF 4202.  FIrst showing of the webcast at 4.  Second showing at 7.  In between I will give a little talk on “Why Open Access is Good for Scientists and the World”.

Hope others will enjoy the day too.  More later …
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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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arXiv reaches 500,000 papers …

Pretty cool that there are 500,000 papers in arXiv (see Slashdot | Free Online Scientific Repository Hits Milestone). Hat tip to Jeremy Peterson for pointing this out. See also Peter Suber on this (Milestone for arXiv)

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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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Nature using Creative Commons license for genome papers

A new paper that just came out by friends and colleeagues of mine from my days at TIGR (Comparative genomics of the neglected human malaria parasite : Plasmodium vivax) reminded me I wanted to blog about how it is a good thing that Nature is using a Creative Commons License for some (maybe all) genome sequencing papers they publish (at least in the main Nature journal). They do not use the fully open CC license that PLoS/BMC use but hey, it is better than many other journals who claim they are making this “Open.”

The license they use is

“This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.”

Too bad they do not do this for all the papers they publish. Maybe Chris Gunter can convince them to do that even though she is now at Hudson Alpha. I think when she was at Nature she helped convince them to do this for genome papers.

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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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Biomed Central sold to Springer

Got to run but thought people might be interested in this story. See the scoop at Scientific American. Will post more later. Open access publisher BioMed Central sold to Springer: Scientific American 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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Rosie Redfield’s Open Access Saga …

Rosie Redfield has an agonizing and interesting series on her blog about her attempts to pay for an article of her’s coming out in the Journal of Molecular Biology to be “Open Access” under the Elsevier OA option (note – this is not fully OA, but it is better than the standard option for this journal). Here are some of her postings worth looking at:

Rosie is one of the true pioneer’s of Open Science, as she has turned her blog into a form of open notebook where she posts discussions about her current research, her papers in progress, grant proposals, and other ideas. Yet the process of trying to pay Elsevier to make her article somewhat more open, and the confusing way “Open Access” is presented by this journal has caused Rosie to (1) give up on the open option for this article and (2) become possibly more enamored with journals that are a bit more committed to Open Access from the beginning.

In her latest post she says

“The Elsevier sponsored-access system is confusing, the policy is not clearly explained, and the necessary information is hard to find.

The Journal of Molecular Biology is an excellent journal, and we’re proud to have our article appear there. The submission and review process went very smoothly, the copy editing was very professionally done, and the 50 free offprints are a nice treat. But I feel strongly that taxpayer-supported research should be published where the taxpayers can see it, so I won’t be submitting to any Elsevier journals in the future.”

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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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Nobel Prize in Medicine Winner is a PLoS One Author …

For You Open Access supporters out there, check out the recent PLoS One paper by Françoise Barré-Sinouss one of the new 2008 winners of the Nobel Prize in Physiology/Medicine.

The paper is Scott-Algara D, Arnold V, Didier C, Kattan T, Pirozzi G, Françoise Barré-Sinoussi, Gianfranco Pancino (2008) The CD85j+ NK Cell Subset Potently Controls HIV-1 Replication in Autologous Dendritic Cells. PLoS ONE 3(4): e1975. doi:10.1371/journal.pone.0001975

You go PLoS One.

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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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