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

UC Davis Bodega Marine Lab getting some props

Now, I have written here before about the spectacular site for UC Davis’ Bodega Marina Lab in Bodega Bay). And lest anyone not believe me, Bodega Bay and the Marine Lab has been written up in the San Francisco Chronicle in an article entitled: Marine lab a spectacular spot on Bodega Bay.

The article lead in is all you really need to know:

Mention Bodega Bay, and the first thing that comes to mind – even now, 45 years later – is Tippi Hedren getting her head pecked by a gaggle of sociopathic seagulls. The town’s visitor center hands out 8,000 maps a year pinpointing where Alfred Hitchcock filmed the most memorable scenes of the 1963 classic “The Birds.”

But each year, 10,000 to 12,000 people travel to a spectacular spot west of town to visit a less-famous site, the Bodega Marine Laboratory, a UC Davis outpost where about 100 graduate students and scientists study underwater life along the Northern California coast.

Each Friday afternoon, from 2 to 4, docents lead free, hourlong tours that wind through parts of the sprawling complex. It soon becomes clear that visiting a marine lab isn’t anything like visiting for-profit aquariums, with their polished tanks and fancy signs. Here, the only live exhibits are a tide pool and three small aquariums.

Mind you, Bodega Bay itself is not the most happening town in the world. But it has a few stores, restaurants and cafes (which they review some of in the Chronicle article). The lab is also the site for the “Workshop in Applied Phylogenetics.” One cool thing about this workshop is that the organizers have begun building a Wiki to gather information on phylogenetic methods and tools and this wiki is open to everyone to use and contribute to. So if you are interested in phylogenetics you might want to check out the wiki and start adding to it. And you might want to keep an eye out for announcements for next years course.

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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 Science Highlight — JoVE: Journal of Visual Experiments

I am starting to browse around at JoVE (the Journal of Visualized Experiments).  This is an open journal dedicated to publishing biological research in a visual format.  It is pretty cool.  Some good videos include ones by Jared Ledbetter’s group on studying microbes inside termites (see Layers of Symbiosis – Visualizing the Termite Hindgut Microbial Community
and Extracting DNA from the Gut Microbes of the Termite (Zootermopsis nevadensis)) for example.  Others of interest to this blog include one by Ed Delong’s group on Large-Scale Screens of Metagenomic Libraries. 
Anyway – JoVE is definitely worth checking out … visual presentations are probably the way of the future …
In addition to experiments, JoVE also has some interviews.  For example, I am embedding a nice video from JoVE with a talk by Ed Delong on microbial communities (Microbial communities in nature and laboratory – interview (Video Protocol).   To view the embedded video click the play button below.

http://www.jove.com/index/embed.stp?ID=202

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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 Darwin won the evolution race

There is a cool article in the Observer today on the “race” between Darwin and Wallace on publishing the theory of natural selection (How Darwin won the evolution race | Science | The Observer).

When I read this I cannot help wonder what would have happened if this race had happened today. With publishing and the spread of ideas occurring at a much slower pace in the past, Darwin could afford a bit of time to polish up all the lines of thought and evidence presented in the Origin of Species. It is really his work on building up such evidence that helped convince people of the importance of natural selection. So – if this had happened today – Darwin and Wallace would certainly have been on Science Friday. Lots of bloggers would have written about it. But would Darwin have taken the time to polish up his loose ends or would he have just rushed out his short paper on natural selection and then gotten caught up in the hype and debate?

Anyway, the article has some good bits both about the history and about the acceptance (or lack thereof) of evolution and natural selection today. My favorite lines is:

Natural selection is simply too important for society to live without it, he (Steven Jones) argues. It is the grammar of the living world and provides biologists with the means to make sense of our planet’s myriad plants and animals

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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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Tree of Life Runners Web Notes 6-20-2008

Just some little notes here in lieu of more detailed posts.


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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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Street View for Davis on Google Maps

If you have not already heard, Google Maps has added the “Street View” function for Davis, CA where they drove around in a truck and took pictures of the front of every address.

See here  for a view of Central Park.

or click on the pic below.

[googlemaps https://maps.google.com/maps/sv?cbp=1,290.12156656153684,,0,5.340041038629993&cbll=38.544852,-121.743822&panoid=-YJgpQoogQqlUEEPmfLcMw&v=1&hl=en&gl=us”>
View Larger Map

Oh – and here I am …. loading my car up for a trip.

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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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Prochlorococcus on Science Friday

Well, I wish I had known this in advance and I would have posted something about it here before last Friday. But anyway – Penny Chisholm (from MIT) and her beloved Prochlorococcus (important photosynthetic marine microbes) were featured on Science Friday last week. Fortunately, NPR broadcast’s like ScienceFriday are a form of Open Access. And you can listen to Penny here. It makes for some good listening — she has some good lines about the importance of microbes as well as the need for more support for work on microbes. She also gives a good plug for the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative (full disclosure – I just got a grant from this program). Note – the Science Friday host makes a bit of a blunder when at the end he asks if they have talked about viruses when a few minutes before she had done exactly that (for more on Prochlorococcus viruses see the Sullivan et al PLoS Biology paper here). You can also get a video of Penny giving a talk 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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Are You Intellectually Clean?

Well, brain doping continues to be an issue, long after the buzz of April Fools Day is over. Now comes what I think must be a spoof of some kind: a site where people can make an “Academic Oath” saying they are clean by putting the following on their CV or WebSite:

For the honour of humanity and the integrity of the academy, I declare I have not, nor ever will, use any drug for an intellectual advantage. See, http://www.academicoath.com

This reminds me a bit of the PRISM spoof “PISD” but I am not sure if Academic Oath is really fake.
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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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Freeing My Father’s Scientific Publications Update

Well, I have made some progress already in my quest I began on Father’s Day to free up the scientific publications of my father (see The Tree of Life: Freeing My Father’s Scientific Publications).

I wrote to the powers that be at the journal “Endocrinology” asking about when back issues might be made available. And I got a VERY quick reply from someone from Highwire Press which is the place that puts out Endocrinology on the web

Dear Jonathan Eisen,

The Endocrine Society is currently in the process of loading back issues for all of their journals. It will most likely be six months before back content is online.

The person who wrote back was almost apologetic about how long this might take but I am personally very pleased. Given that Endocrinology says the make all articles more than a year old available for free, this likely means that my father’s three papers in Endocrinology will soon be available for free online. This then changes my tally to:

Pubmed Central: 3
Free access: 17
Fee access: 11
Unavailable: 4

Getting better. Of course, I want them all to be as widely available as possible so I am still going to work to move everything up the list towards Pubmed Central. Also, my brother suggests (in the comments to my previous post) that since my father was a government employee we should be able to just post his papers online. I think this is a good option but I still will be working on the “official” channels to see what happens.

Since I made the original posting there have been some useful comments about what I might do on some other sites. See for example, this FriendFeed discussion (I have just discovered FriendFeed and it seems quite cool but I am not sure if everyone can see this discussion or not so please let me know if this link does not work).

I will keep posting on my progress as well as what I learn about Copyright, Free Access, etc.

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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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ASM Bloggers Breakfast and Lost Notes

Oops.  I wrote some additional notes to post for the ASM Meeting but seem to have deleted or misplaced the file.  One of the things I wanted to write about was how glad I was to have dropped by Moselio (aka Elio) Schaecter’s breakfast discussion of blogging and microbiology.  Fortunately Moselio has posted about this on his wonderful “Small Things Considered” Blog.  I note it was also good to finally meet Tara Smith, who also has a great blog “Aetiology” and to meet/remeet some of the others.  I was also inspired by some of the people there to start rebuilding my “OpenWetWare” lab page.   Though I arrived late, the breakfast for me was the most inspiring thing about the whole meeting …

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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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Tree of Life hitting the big screen …

The “Tree of Life” is really hitting the big time. I just found, in a google search, that there is a movie coming out in 2009 called, “Tree of Life (2009).” The plot summary is as follows:

In a mystical world of folklore, several individuals embrace in a race to find the Tree of Life, said to give immortality, fertility, and other supernatural powers

And if that does not excite you, well, maybe this will. The cast includes Brad Pitt, Sean Penn and a few other big shots. Stay tuned here for more updates, or check out the wikipedia page for the movie here. Also see: Brad Pitt and The Tree of Life, Brad Pitt Scales Tree of Life,  Malick’s Tree of Life caught on camera, Brad Pitt looks young in Tree of Life movie

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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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