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

Evidence Based Healthcare and Baseball

Love the Op Ed piece in the Friday New York Times entitled “How to take American Healthcare from Worst to First.”  First, one reason I love this article is it is discussing how we need to move to more “Evidence Based” medicine.  You may be amazed to know that much of medicine is not evidence based but that is the sad truth.  When I first heard about how not all medicine was evidence based medicine (in a talk by David Cox when I was a grad. student) I was blown away.  Anyway, the article is worth a read from this point of view.  

More amazingly is the author list — Billy Beane (general manager of the Oakland A’s), Newt Gingrich, and John Kerry.  What a combination.  They make the argument that medicine needs a wholesale change in the way it is done just like baseball is shifting to more evidence based decisions.  It is a nice analogy.  Too bad the current administration believes that simply thinking about something is the equivalent to evidence.  And also too bad that McCain-Palin seem to be following in the trend of Bush to not hold “evidence” in high regard.  I wonder what Newt (who is a big science and technology advocate) thinks of the recent anti-science push of the Republicans in power.
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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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McCain Palin going after fruit flies

As if scientists did not have enough reasons to vote against McCain-Palin who seem to have decided that Bush was overly supportive of science. Now Palin is attacking of all things “fruit-fly research.” Lovely. Proof that they are both clueless (not knowing what a fruit fly is probably) and anti-science at the same time. For more on this see:

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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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Brain Doping April 1 Joke still getting some press

Well, my April 1 collaborative joke on brain doping is still getting some press. See El Pais which reports

Como muestra, algo que empezó como una broma. “Los centros del NIH (los Institutos de Salud de Estados Unidos) pedirán a todos los científicos que quieran optar a sus ayudas y subvenciones a que pasen pruebas antidopaje para comprobar que no han tomado estimulantes cognitivos para aumentar su rendimiento intelectual”. Una supuesta World Anti-Brain Doping Authority (WABDA) se encargaría de los análisis. Es el mensaje de una nota de prensa falsa. Una fake lanzada en Internet el pasado 1 de abril, el día de los inocentes en Estados Unidos, por Jonathan Eisen, biólogo evolucionista de la Universidad de California. Comenzó como una travesura, pero el rumor acabó por extenderse por la red.

La broma apunta, sin embargo, a un debate abierto entre la comunidad científica. Si se controla el dopaje en deportes como el ciclismo, ¿por qué no controlarlo en la comunidad científica, donde también compite el intelecto por conseguir becas, ayudas e incluso premios en reconocimiento de su inteligencia? Esa era la reflexión original que, según explica Eisen, le llevó a colgar su broma de Internet. Sin embargo, también afirma que nunca aceptaría que se realizasen ese tipo de controles.

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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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Roan Press Web Site Live

Well, I wrote about Roan Press (“Sacramento’s Small Literary Publisher”) a while ago (see here) since a friend of mine from grad. school Brad Buchanan had published a new poetry book through them and was on the air on KDVS.  And now the Roan Press web site is live.  You can order Brad’s book Swimming the Mirror there (and see a review here).  Brad will be doing a reading at the Avid Reader in Sacramento (1600 Broadway) at 1 PM on October 26. 

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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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Blocked Access Bummer #1

I have decided to start posting when I want to read an article at home but cannot due to lack of access (even though I might have it at work).  Today’s bummer is I wanted to read an article by Joel Sachs on “Resolving the first steps to multicellularity” but I could not get it because I do not have access to Trends in Ecology and Evolution at home.  Bummer.  Looks like it could be good. 

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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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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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At Davis Today – Chris Somerville on Cellulosic Biofuels

Quick Post Today — For THose Interested in Biofuels — you might be interested in this

Distinguished Lecturer
Dr. Chris Somerville
Director, Energy Biosciences Institute (EBI)
Presents On:
“Cellulosic Biofuels”
UC Davis ARC Ballroom October 16, 2008, 3:00-4:00 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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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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