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

Article in the Christian Science Monitor on PLoS One and related topics

Just saw an interesting article in the Christian Science Monitor on the “end of the scholarly journal” which talks quite a bit about PLoS One. Definitely worth checking out — many quotes from Chris Surridge of PLoS One and some discussion of Blogs and related sites.

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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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Antibiotic resistant bacteria plaguing US soldiers in Iraq

Very interesting article in Wired magazine about an antibiotic resistant bacteria that is plaguing US soldiers in military hospitals in Iraq. It’s got some stuff I would disagree with in there about gene transfer and evolution but overall this is a really good and interesting article about bacterial evolution and antibiotic resistance.

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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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Interesting (but misguided) letter to the editor

There is a funny/interesting letter to the editor in one of the local papers out here. It is basically about how an article on Neanderthals is interesting but how more should be written about current topics in evolution, which sounds great. Then the author proceeds to quote Fisher and Morgan regarding human evolution, not the most modern of research to quote. Anyway, the calculation they made I found to be quite interesting …

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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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Blog apologies — evolution happens

Well, sorry for the limited number of postings here recently. I am working on increasing my own fitness — we have a baby due next week and my blog has fallen a little behind. I will get back into blogging more in about 3 weeks. If I see anything interesting before then I will post but there may still be a short lull. Now back to getting 1,000,000 things done in one week.

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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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Genomics Gets Nasty

Just saw an entertaining press release about the publication of the genome of the parasite Trichomonas vaginalis. I find this entertaining because it does a remarkable job of capturing the personality of Jane Carlton, the PI on the project, who I used to work with at TIGR.

I particularly like the end

Viewed under the microscope Trichomonas vaginalis moves quickly; it has four undulating flagella and a tail. “It is a gassy organism,” says Dr. Carlton. It has special power-generating structures called hydrogenosomes. They produce hydrogen. “So it is releasing hydrogen into the liquid media, making it frothy,” she says. “That is why the vaginal discharge is frothy.”

The pathogen grows easily in the lab in test tubes containing some liquid media. And it has, as she says, “a real yuck factor to it.” A good way to know the microbe is growing well is to smell the contents of the test tube. “It smells foul, it has a fishy odor; really nasty,” says Dr. Carlton. “My technician used to get grossed out by that.”

While it is true that Jane has no fear about saying things that make some people uncomfortable, it is entertaining to the it in the NYU press release.

The press release is worth reading for another reason – the history of this genome project is different from many other parasites. In this case, the genome was enormously bigger than had been predicted (usually they are smaller than predicted, in part becuase if you over predict the genome size, you will have some extra money in your grant to cover other issues). The press release gives a good impression of how much of a pain it is to run a genome project sometimes.

Anyway – back from a little layoff and just wanted to say – good job Jane.

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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 Education?

Thanks to Jacques Ravel for pointing this out. U. C. Berkeley has begun posting many of its science classes as Podcasts which are avilable for download at a special Apple Itunes Site. Also posted are some lectures such as one by George Smoot who just won one of those Nobel Prize thingies. It seems Stanford is doing a similar thing although it does not seem as extensive.

Note sure what other Universities are doing this (I know some classes are podcasting but not clear how many Universities are doing it as extensively as Berkeley).

If anyone else knows of other such efforts please let me know (also see this list of free academic podcasts).

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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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My Open Access New Years Resolutions

Well, 2006 is over and in terms of Open Access to Biomedical type publications, I think it was a pretty good year. The papers being published in Open Access journals continue to get better and better and there are more Open Access journals too. Perhaps to biggest new thing from last year was the start of PLoS One, which is not only an Open Access journal but one that is experimenting with a new type of peer review system.

But of course, more needs to be done. So I am posting here my personal list of Open Access New Years resolutions. These are things I hope to do and hope to convince others to do too (these are in no particular order).

1. Convince more collaborators to publish papers in Open Access journals.

2. Release more of my labs data in a more usable format to Open Data archives (see Bill Hooker’s Open Reading Frame blog for more details about doing this).

3. Discuss Open Access to publications and data in all my scientific presentations/talks.

4. Write more blogs about Open Access and its benefits.

5. Convince some existing journals to switch to a more Open Access stance (e.g., I wish this would happen with Journal of Molecular Evolution — I resigned my position as an Academic Editor when they would not shift but there is still hope).

6. Submit as many of my past papers that were not in Open Access journals to self-archiving repositories (see the comments on my previous blog about this – it seems that this is possible even for Nature papers).

7. Work with Pubmed Central to make self archiving possible there for more papers. Right now it is only possible to submit your own work to Pubmed Central if it was NIH or Wellcome Trust funded.

8. Discuss Open Access with more scientists. Some still have notheard about it and some do not realize what the issues are.

9. Discuss Open Access with more non scientists. To get Congress to pass more rules regarding Open Access, it will help to have more pressure from non scientists. When I have described the current publishing system to non scientists, they are usually astonished by the (1) wasted money and (2) closed nature of much scientific work.

10. Work to get researchers who publish in Open Access journals “extra credit” in promotions, tenure review and grant proposal review. These people are frequently taking risks for the betterment of the scientific community and to advance scientific knowledge. They deserve credit for taking these risks.

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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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PLoS One Beta is released – a new way to publish and discuss scientific papers

Well just got an email from Chris Surridge of PLoS One saying their Beta Site is open to the public. I am excited by this new journal and system and plan to submit many of our papers there. People should check it out for themselves and hopefully give comments to them to make the system better. Some detail from the email is given below.

The first paper there that struck my eye is a paper on polyploidy in halophilic Archaea. This paper, by Sebastian Breuert, Thorsten Allers, Gabi Spohn, and Jörg Soppa suggests that polyploidy is more common in archaea than was previously appreciated.

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The email says:

Before your first visit, I want to let you know about the inherent challenges of this project and the philosophy that compels PLoS to confront them.

We want to speed up scientific progress and believe that scientific debate is as important as the investigation itself. PLoS ONE is a forum where research can be both shared and commented upon – we are launching it as a beta website so that the whole scientific community can help us develop the features.

What makes the site beta? Not the content, which features peer-reviewed research from hundreds of authors across a diverse range of scientific disciplines. It’s the additional tools and functionality surrounding these papers that will be continually refined and developed in response to user feedback.

It is this union of continually evolving user tools provided by the Topaz publishing platform and extensive content that will make PLoS ONE a success.

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The first beta release of PLoS ONE features tools that allow users to annotate articles and participate in discussion threads. Our goal is to spark lively discussion online and we’d like to invite you to participate. Future updates will include user ratings for both papers and the comments made about them, personalized content alerts and much more.

We will be watching with interest to see how our new platform and software responds to high volumes of traffic and encourage you to give your feedback on your first experience via the site itself.

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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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Check out Open Reading Frame Blog on Open Data

Here is an Open Access must read. Bill Hooker blogs about pushing the Open Access envelope in the area of Open Data. That is, making sure the raw data from a scientific study is available. Although there are many efforts for this, he discussed something I have never really considered which is trying to make sure the journals do not somehow obtain rights to the raw data (e.g., by having it placed onto their site as Supplemental Information).

He has a suggested protocol for adding an addendum to the typical copyright agreement one might make with a journal, which is, in my mind, a great first step.

So go read about it 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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Microbes, Minerals, and the Environmen – Abelson Lectures

I just had this site pointed out to me by Merry Youle.

This site is a collection of audio and video of lectures that were for the “Microbes, Minerals, and the Environment” symposium. The collection includes talks by David Stahl, Derek Lovely, Anna Louise Reysenbach, Faroq Azam, Jonathan Zehr, and Paul Falkowski, all relating to microbes in the enviornonment. I have not watched all of them but the ones I have seen are quite good.

The symposium was in honor of Philip Abelson, who died in 2004.

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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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