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

Trip to Sacramento Zoo got interesting with man’s head getting stuck in photo booth






Well, went to the SacZoo with my daughter on Tuesday. Not the best zoo in the world, but it is a perfect size for her right now. She loves the Koi Pond in particular (but also the big cats and the flamingoes). The strangest part of this last visit was the guy who got his head stuck in the wooden animal cutout that you can have your picture taken in (you know, you stick your head through and take a picture from the other side).

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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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Flock of Dodos – Evolution vs. Intelligent Design

Well, Randy Olson has done it again. Flock of Dodos is his new film. It is about the Intelligent Design vs. Evolution Debate and from what I can gather it skewers both sides of this issue quite a bit.

Randy was the head of Prairie Starfish Productions, which made some of the dorkier and funnier science moves I have ever seen including one about Loster Fisherman in New England. I first met Randy while on a Deep Sea cruise in the Gulf of Mexico where he was filming my then advisor Colleen Cavanaugh for a film about women scientists. He and I played some mischief on her associated with her first deep sea Alvin dive where we made a video of her stuffed panda being tortured.

But that is beside the point, Randy is really good about seeing through some of the facade of seriousness in science to get to the absurdities and dorkiness of some aspects of science.

So I suggest people try and check out his new film which is being screened around the country on Darwin’s birthday next 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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Harold Varmus goes truly Open

Harold Varmus, one of the CoFounders of the Public Library of Science, has been featured on a NIH Profiles site. Through this site they are making a collection of his papers freely available. In addition, to co-founding PLOS, Varmus won one of those Nobel Prize thingies and was head of a little place called NIH.

Not that much is featured on the front pages. But if you go to the search page here you can search for all sorts of interesting stuff.

Some interesting ones I found:

I will post more when I have a chance but if anyone else sees interesting ones out there please post them too.

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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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Evolution in action – Dog Breed Hybrids in NY Times

Excellent article in the NY Times Magazine this weekend on hybrids of purebred dogs.

It is basically a lesson in microevolution, inbreeding, and modern genetics. Some great lines are found throughout including

Havens moved on, like some strange Noah touring his ark — in which every tidy two-by-two had been split apart, jumbled and recombined into a single animal: “That’s a Chihuahua-bichon . . . here’s a half-American Eskimo and half-Lhasa apso” — his voice lifting each time as if to ask, What will they think of next? But he had dreamed up a lot of these things himself.

AND

Dogs with separation anxiety are now commonly treated with psycho-pharmaceuticals. Maybe re-engineering the dog itself, hybridizing newer models, represents “the last piece of the puzzle,” Bob Vetere says. “Will they reach a level of convenience where you have a postage-stamp-size dog that makes you dinner when you come home and reads the paper to you before you go to bed? I’m not sure that’s going to happen. But certainly someone’s going to try it.” After all, the dog, which we’ve molded into one of the most physically diverse mammalian species on earth, has so far been uncommonly obliging to our needs. Why shouldn’t we be capable of driving the entire species toward its inevitable end, down a millennia-long trajectory from wolf to stuffed animal?

The blade runner future is nearly with us … what is to stop more and more twisted projects from happening? Nothing really. I mean, dog breeds are already freakish. With a little extra push, they will just get more bizarre. The really bad part of this is that the breed dogs and then kill the puppies that don’t cut it for whatever their goals were. That has been happening for ages but it still saddens me.

Despite some depressing aspects of the article, it is a good read.

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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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3rd International Metagenomics Meeting

Just got this by email —

Dear colleagues,

We are pleased to announce that the Annual International Metagenomics Conference (Metagenomics 2007 ) will be held July 11-13, 2007, at Atkinson Hall (Calit2) at the University of California, San Diego, California (U.S.) The meeting will kick off with a networking reception and keynote presentation the evening of the 11th (Wed), followed by a full-day meeting on the 12th (Thurs) and a half-day meeting in the morning and a half-day tutorial/demonstration in the afternoon on the 13th (Fri). This is the second meeting in San Diego and the third international metagenomics conference since Metagenomics 2003, which was organized by Dr. Christa Schleper in Germany. We will update information on the meeting via this mailing list. For more information, please visit the conference website at http://www.calit2.net/metagenomics2007 .

Best wishes,
Kayo

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Kayo Arima, PhD.
University of California, San Diego
California Institute for Telecommunication and Information Technology
9500 Gilman Dr. La Jolla, CA 92093-0440
Office: 858-822-4649
Fax: 858-822-5033

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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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Science World Coming …

The US Department of Energy and the British Library announced an agreement to develop a new international science portal aimed at sharing scientific information. It sounds like a great thing. Now if only DOE would require Open Access publishing of scientific research that they fund … that would really show DOE’s committment to Open Science. I recommend sending Dr Raymond Orbach, who is leading this initiative, an email message, the address for which you can find at this link at the top of the page.

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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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Synthetic Biology (faculty job available at U. C. Davis in the Genome Center)

Just heard another talk by Drew Endy about Synthetic Biology and his attempts to make the field work more like Engineering than Biology. Basically, what he is trying to do is to make biological parts (e.g., Biobricks) at the DNA level that would work like circuitry board parts do for making computer chips and related devices. As they get more biological parts, more people will be able to treat synthetic biology in an abstract way – that is they will not need to know per se how the biological parts work, just that they have particular properties.

My favorite part of the field of Synthetic Biology is IGEM, the The international Genetically Engineered Machine competition. Students compete to make cools things from their biological parts. Among the more interesting items that have been made is a bacterallawnthat work as a camera.

In general, I like synthetic biology and the potential it has to produce major benefits for the world, although I wish some of the practitioners were less flippant about the potential risks in the field. And, this minor blog would not be complete without the self interest. THe UC Davis Genome Center has just announced a new faculty position in this area (specifically in cmputational and experimental approaches to network and synthetic biology). So if you are in this field and want to join a great collection of faculty working in diverse areas of genomics, please apply.

Job at Davis

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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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Non Open Access publishers getting desperate

Well, this kind of made my day. Nature is reporting that a group of non open access publishers have hired Eric Dezenhall to help them with public relations. Eric Dezenhall is a crisis management consultant (as well as a fiction author) who many may demonize but he certainly seems to be good at what he does. The article at Nature is worth checking out and points to the desperation of these publishers when they see the writing on the wall regarding Open Access. For example, Nature reports a person at AAP the Association of American Publishers says:

“We’re like any firm under siege,” says Barbara Meredith, a vice-president at the organization. “It’s common to hire a PR firm when you’re under siege.”

Keep up the siege everyone. Their ship is sinking and they are grabbing at the last little pieces of wood they can find.

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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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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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