Eisen Lab Blog

Post Doc in quantitative modeling of viral dynamics and evolution

A postdoctoral position in quantitative modeling of viral dynamics and evolution is available under the direction of Prof. Joshua Weitz (School of Biology, Georgia Tech). The postdoc will work in an interdisciplinary research group of biologists, physicists, and computer scientists. The postdoc will collaborate on research focusing on bacteriophage dynamics and evolution, at the molecular and ecological scales. Specific project goals will be to develop gene regulatory models of viral exploitation and link intracellular dynamics to long-term changes in viral functional traits at the population scale. The postdoc will also have the opportunity to develop new research projects at the interface of systems biology, theoretical ecology & dynamical systems.

The position will provide competitive salaries and benefits. The postdoc will be based in the School of Biology at Georgia Tech, with a preferred start date of September 2009, though the start date is flexible. The initial appointment will be for one year, with renewal up to three years subject to satisfactory progress and mutual agreement.

REQUIREMENTS: (1) PhD in computational biology, physics, mathematics, microbiology, ecology or related area; (2) Demonstrated research excellence; (3) Strong quantitative skills; (4) Strong oral and written communication skills. Ideal candidates from the biological sciences should have experience with scientific programming. Ideal candidates from the physical/mathematical sciences should have prior exposure to research in the biological sciences. However, outstanding applicants looking to broaden their field of interest will also be considered.

TO APPLY: Applications should be emailed to jsweitz(at)gatech.edu and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, and continue until the position is filled.

ABOUT THE GROUP: The Weitz group is supported by grants from the Burroughs Wellcome Fund, the James F. McDonnell Foundation, DARPA, and the National Science Foundation. For more information, consult the Weitz group website or contact Joshua Weitz: jsweitz(at)gatech.edu.


More information is available at: http://ecotheory.biology.gatech.edu/
——–
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.

——–

Michael Ashburner or Francis Ford Coppola in the New York Times?


Imagine my surprise when I opened the New York Times a few days ago and saw a giant picture of Michael Ashburner the Drosophila genomics guru, open science advocate, and Won for All author. Now, Ashburner is one of my favorite people in all of science (see my posting from a while ago recruiting him top start a blog to which he even responded). I mean, sure, people I know are in the Times everyonce in a while but this was astonishing. Here he was in some sort of fashions of the Times type of section, shirt unbuttoned, lounging in some field.

Alas, closer examination and some google searching found the truth. This is alas not Ashburner, but actually Francis Ford Coppola and his daughter Sofia. But I mean – look at the pics of Ashburner below. It really could have been him. Oh well, maybe next time …


——–
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.

——–

Archaea get no respect from the New York Times

There was kind of funny and certainly interesting article in the New York Times on June 4: Greening the Herds – Trying to Limit Cows’ ‘Emissions’

The article by Leslie Kaufman discussed how there are attempts in some dairy farms in the US to change the diet of cows to reduce their methane output. The methane is a strong greenhouse gas and in total cows make a surprisingly large global contribution to greenhouse gases. The article states:

Cows have digestive bacteria in their stomachs that cause them to belch methane, the second-most-significant heat-trapping emission associated with global warming after carbon dioxide.

Alas, this is not correct. Yes, bacteria in the cow rumen contribute to the production of methane. But they do not make the methane. The methane is made by archaea (for those not in the know, archaea are a distinct group of organisms relative to bacteria – they resemble bacteria in many ways but are a separate branch on the tree of life). For those of us who study archaea this is a major slight. A diss. A taunt. A sad day. And all those other things. Not sure how we archaea fans will have our revenge but I swear we will. Too bad Carl Zimmer does not think that this is important enough to go on one of his newspaper fact chekcing investigations.

——–
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.

——–

David Byrne on Bicycling and Davis in the New York Times

For those of you who are obsessed with bicycling (like me), and live in bicycling heaven Davis, CA, and occasionally look at the New York Times, you may have noticed this already. But for others who have not I want to call your attention to a book review in the New York Times this past Sunday by David Byrne Book Review – ‘Pedaling Revolution – How Cyclists Are Changing American Cities,’ by Jeff Mapes – Review – NYTimes.com.

Amazingly this is indeed the same David Byrne of them Talking Heads. It turns out he has a book coming out in the fall called “Bicycle Diaries.” Anyway he reviews this book on the effect of bicyclists on American Cities and right there in the review are some props for my town, Davis, CA. The article is worth checking out and I will both be buying this book and awaiting Byrne’s. Maybe we can have a reading here in Davis when the Bicycling Hall of Fame opens its doors.

——–
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.

——–

Children’s Science Books from NY Times 5/10/09

Better late than never I guess.  I missed the NY Times Children’s Books section in teh 5/10 Book Review but my mother brought it with her and left it so I am posting a tiny bit about it.

They review/suggest a few books for kids and many of them have a theme related to this blog including:
——–
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.

——–

Art-Science Fusion and Darwin’s Face at Davis

ART/SCIENCE FUSION STUDENTS EXHIBIT PHOTOGRAPHY AND A CERAMIC MOSAIC MURAL, THE FACE OF DARWIN

The final student exhibition for “Photography: Bridging Art and Science,” a Science and Society Program class taught by Terry Nathan as a part of the Art/Science Fusion series at the University of California, Davis (UC Davis), will be held at the Buehler Alumni and Visitors Center on the University of California, Davis campus beginning June 3 and continuing through July 3. The exhibit features over 50 student photographs exploring the conceptual connections between art and science and the role of art and science on the UC Davis campus. The opening reception, which is free and open to the public, is June 4 from 3-5 p.m.

Also included in the exhibition is a ceramic mosaic mural, The Face of Darwin, created by students and community members in a special Freshman Seminar entitled, “The Face of Darwin: Exploring the Art/Science Borderland”. In recognition of Darwin’s 200th birthday, students from majors across campus studied Darwin’s life and the observations that led him to propose evolution by natural selection.  Darwin’s face is formed by selections from his secret notebooks and the images of those organisms that influenced him most.  With a beard of peppered moths, hair of barnacles and a coat of iguanas, finches, orchids and a host of other creatures, this mosaic is a profound learning experience in and of itself. The seminar was led by Diane Ullman and Donna Billick (co-directors of the Art/Science Fusion Program). 

(this came in an email to me and am posting here)

——–
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.

——–

Junk mail and trash associated with science

Just got back from the ASM Meeting that was in Philly last week.  It was good and bad – and will write more about it soon.

But what I am writing about now relates to an annoying part of the meeting.  It seems ASM has sold my name/address to various entities since I have been receiving a significant amount of junk/trash advertising things associated with microbiology.  I am sure ASM gets some $$$ out of this, but at what cost to the world?  The last thing I want is more trash and there seems to be no way to say no to this.  
And on top of it, many science related publications also seem really keen on wrapping themselves in plastic.

http://picasaweb.google.com/s/c/bin/slideshow.swf

In this case I am showing Nature Methods and the ASM Microbe and even the HHMI magazine  wrapped in plastic. Bad Nature. Bad ASM. Bad HHMI.  Sure there may be reasons for this (e.g., maybe they have an insert), but there must be non plasticy solutions.  And fortunately the news from the JDRF has no plastic. Good JDRF.  Here’s to sciency publications getting a little greener.

——–
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.

——–

Good science education resource: HHMI Cool Science

Just a quick one here. Was reading the HHMI Bulletin and saw a note about this web site they have set up on science education (see Cool Science: Home). It has all sorts of goodies for educators, kids, and others. Some of my favorite things there in looking so far include material from the Genome Consortium for Active Learning (GCAT) and the Biointeractive page. YAGTFH (Yet another good thing from HHMI).

——–
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.

——–

Do not fall for SPAM pretending to be from Elsevier

Just got the email below (with some key parts blotted out). It is clearly (to me) fake (although it is kind of funny in a way given the recent news about Elsevier publishing fake journals). But just in case someone else out there got the same SPAM and did not figure out it was fake, I am posting this message here.

ELSEVIER:
BUILDING INSIGHTS; BREAKING BOUNDARIES
MANUSCRIPTS SUBMISSION

Dear Colleague,

On behalf of all the Editors-in-chief of Elsevier Journals, we wish to Communicate to you that we are currently accepting manuscripts in all Fields of human Endeavour.
All articles published will be peer-reviewed. The following types of papers are considered for publication:

• Original articles in basic and applied research.
•Critical reviews, surveys, opinions, commentaries and essays.

Authors are invited to submit manuscripts reporting recent developments in their fields. Papers submitted will be sorted out and published in any of our numerous journals that best Fits. This is a special publication procedure which published works will be discussed at seminars (organized by Elsevier) at strategic Cities all over the world. Please maximize this opportunity to showcase your research work to the world.

The submitted papers must be written in English and describe original research not published nor currently under review by other journals. Parallel submissions will not be accepted.

Our goal is to inform authors about their paper(s) within one week of receipt. All submitted papers, if relevant to the theme and objectives of the journal, will go through an external peer-review process.

Prospective authors should send their manuscript(s) in Microsoft Word or PDF format to XXXXX and should Include a cover sheet containing corresponding Author(s) name, Paper Title, affiliation, phone, fax number, email address etc.

Kind Regards,

XXXXXXXXX

PS: Pls. show interest by mailing XXXXXX if your Manuscript is not ready but will be ready soon.

——–
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.

——–

Fun at Novozymes in Davis

Normally, I hate marketing slogans.  But I must say I was pretty happy with the way Novozymes portrayed its “Rethink Tomorrow” branding.  Yesterday, I went over to Novozymes in Davis for the opening of a new building (Novozymes has an R&D branch in Davis).  It was a short and nice ceremony that included presentations by honchos from their HQ, some local Novozymes employees, as well as folks from the community including the Mayor Pro Tem of Davis Don Saylor and the head of the UC Davis Genome Center where I work, Richard Michelmore (who also happens to be the Novozymes Chair of Genomics).

What I liked about the marketing/branding discussion was how Novozymes is focused on making enzymes that can reduce the environmental impact of various industrial, agricultural, and personal processes like the making of biofuels.  Sure, everyone is going green these days or attempting to in some way.  But their argument that custom designed enzymes can reduce waste, allow for lower environmental impacts, etc, made sense to me.  In addition, they made significant efforts to make their building a low impact building.  Sure, nobody is perfect, but Novozymes seems to be making significant efforts towards the greater good even when they do not have to.  
Of course, perhaps I am a little biased since I live off Novolog from NovoNordisk, a “sister” company of Novozymes (see picture at the end of my slide show on my Novolog pen …).  

http://picasaweb.google.com/s/c/bin/slideshow.swf

See also

——–
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.

——–