Eisen Lab Blog

U. of California seeking proposals on UC-Industry collaborations

Just got this email that might be of interest to some:

The University of California Office of Research and Graduate Studies is pleased to announce the spring 2010 UC Discovery Grant Request for Proposals.

The University of California Discovery Grant opportunity (UCDG) promotes collaborations between UC researchers and industry partners in the interest of supporting UC researchers and trainees, strengthening the state’s economy, and serving the public good. The UCDG is a matching grant mechanism; research projects are jointly funded by a UC Discovery Grant and a required industry matching contribution.

All applicants must submit a Notice/Letter of Intent (LOI) between January 11-February 12, 2010. Full proposals are due on March 2.LOIs and proposals must be submitted using the online proposal system proposalCENTRAL https://proposalcentral.altum.com/. Please refer to the program website for the most up-to-date information: http://www.ucop.edu/ucdiscovery/ . Detailed LOI and Application submission instructions will be available at the website above and on proposalCENTRAL the beginning of January.

Please circulate this announcement widely.

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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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So cool – CoPI/colleague of mine Jessica Green picked for TED2010

I am so incredibly psyched that my colleague, collaborator and friend Jessica Green was picked for the TED2010 conference. See the press release here.

Jessica is a Microbial Ecologist at U. Orgeon and has a diverse background in engineering, biology, physics and other things.

And she is both brilliant and cool.  They could not have picked better.  Way to go Jessica.

Want to know more about her work.  Watch this video:

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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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Nice Darwin Art at #UCDavis Evolution/Ecology Dept.

For more on this see The Face of Darwin where K. Garvey explains the history of the mural in more detail. 

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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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Great call for more openness in biology discussions by Steven Wiley in the Scientist

An article after my own heart … Steven Wiley has written a column in the Scientist (Speak Your Mind :The Scientist [2009-12-01]) that speaks both to me and for me. In it he discusses the need for biologists to be more public about their opinions about their work and that of others.

He says, for example

Recently, I attended a conference on biofuel development that included a discussion of the feasibility of deriving fuels from algae. In the open meeting, only a few biologists voiced an opinion, all stated very politely. In private, however, the opinions that I heard were invariably strong and contentious, and few people agreed with what appeared to be the general consensus. It seemed that most of the meeting participants were unwilling to let their viewpoints be publicly known.

I have witnessed the exact same phenomenon and find it disheartening. To help build science and biology we need to be more open about discussing ideas. This pattern of whispering behind the scenes or standing behind anonymity drives me a bit crazy and it is one of the reasons I have become a science blogger and tweeter and such.

Wiley wraps up his discussion by saying

However, a comment is only really useful when the author is identified, because it allows you to evaluate its credibility. Besides, why should anyone respect an opinion that even the author is not willing to claim? And being honest does not mean being insulting or nasty. Open and honest debate has always been necessary for the best science, but mutual respect between the participants is necessary to make it work.

I agree with this too. I have slipped occasionally in being too nasty in comments but am trying to get that under control. But overall, the importance of openness far outweighs the risk of sometimes being offensive. So I am calling for others in biology – start a blog – start tweeting – ask more questions at meetings – get up and say you what you think – sign your name to reviews – sign your name to comments on the web – be more open. It will be good for all of us.


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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.

——–

Amazing post-doc fellowship opportunity: Center for population biology at #UCDavis

No bias here — but this really is an incredible post doc opportunity in population biology here at U. C. Davis. See below:



EFFECTIVE: December 7, 2009
DEADLINE: January 20, 2010
POSTDOCTORAL FELLOW IN POPULATION BIOLOGY–The Center for Population Biology at UC Davis invites applications for a Postdoctoral Fellowship in Population Biology, broadly defined to include ecology, phylogenetics, comparative biology, population genetics, and evolution. We particularly encourage applications from candidates that have recently completed, or will soon complete, their PhD. The position is for TWO YEARS, subject to review after one year, and can begin as early as 1 July 2010. It has an annual salary of $38,000 plus benefits, and $6,000 per annum in research support. The Fellow will be a fully participating member in the Center for Population Biology and will be expected to have an independent research program that bridges the interests of two or more CPB research groups. We strongly encourage candidates to contact appropriate faculty sponsors before applying. We also ask that each Fellow teach a multi-day workshop, discussion or lecture series that is of broad interest to the community of population biologists at UC Davis; faculty sponsors or the Director of CPB, Jay Stachowicz, can provide additional input on this aspect of the fellowship. For samples of past workshop abstracts and more information about UC Davis programs in population biology, see http://cpb.ucdavis.edu/jobs.htm.
ONLINE APPLICATION: Interested candidates should submit a cover letter, CV, a short (1-2 page) description of research accomplishments, a short (1-2
page) description of proposed research including potential faculty mentors, a brief description of their proposed workshop/minicourse, and copies of two publications at http://www2.eve.ucdavis.edu/jobs/ all as PDFs. We require 3 letters of recommendation. The referees you list in the online application will receive an automatic notification from our system instructing them how to directly upload letters to our website. Refer to the on-line instructions for further information. For full consideration, applications should be received by January 20. 2010. The University of California is an affirmative action/equal opportunity employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences. E-mail questions to gradcoordinator@ucdavis.edu.
DEADLINE: January 20, 2010
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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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HHMI Biodiversity Talks 12/3, 12/4 reminder

Reminder – – UC Davis Alumni and brilliant microbiologist Bonnie Bassler will be giving one of the HHMI Holiday Lectures on Science as a WebCast. Anyone can watch Dec 3 and 4th. She will be talking with Baldomero Olivera and the topic(s) will be “Exploring Biodiversity: The Search for New Medicines”. See HHMI’s BioInteractive – Holiday Lectures on Science for more detail.

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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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Single cell genomics gets its own Center at the Bigelow Lab

Just got this email announcement:

Dear colleagues,

We are pleased to announce the establishment of the Single Cell Genomics Center (SCGC) at the Bigelow Laboratory for Ocean Sciences. The goal of SCGC is to make single cell genomics more accessible to the broad scientific community and to serve as an engine of discoveries in the areas of microbial ecology, evolution, and bioprospecting. The SCGC works as a shared user facility, available to scientists at Bigelow and other institutions, with user fees charged to cover SCGC operational costs. For more information, please see our website:

http://www.bigelow.org/research/facilities/single_cell_genomics_center/

We also want to draw your attention to the upcoming second Microbial Single Cell Genomics Workshop, scheduled for September 19-24, 2010:

http://www.bigelow.org/research/facilities/single_cell_genomics_center/workshop2010

With best regards,

Ramunas Stepanauskas and Michael Sieracki 

Single cell genomics is clearly moving up in the world and this is further proof — a whole core facility dedicated to providing single cell genomics to the world.  I note, I have collaborated with Ramunas and others on a recent PLoS One paper on single cell genomics (see Woyke T, Xie G, Copeland A, González JM, Han C, et al. (2009) Assembling the Marine Metagenome, One Cell at a Time. PLoS ONE 4(4): e5299. doi:10.1371/journal.pone.0005299). 


Basically the idea is, that sequencing and/or characterizing the genomic content of single cells is going to be a powerful tool in many areas of biology research … including studies of microbial communities, interpreting metagenomic data, studies of mutation processes, population genetics, 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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Open letter from the Academic Council to the UC (U. California) community

Just got this in my email with a comment to feel free to disseminate it widely.  So here goes:

Open letter from the Academic Council to the University of California community

 

We are the Academic Council of the University: we are the chairs of the ten campus divisions, as well as the chairs of the systemwide committees. We write to address the protests on many of UC campuses over the Regents’ decision to increase student fees by $2,500 per year. This decision followed budget shortfalls that have entailed significant staff layoffs and cuts to a range of student services. Faculty and staff also are suffering from significant reductions in compensation due to the current year’s salary reductions and furloughs.

 

We share the anguish over the policies adopted in the face of the state’s abrupt 20% disinvestment in higher education. The budget shortfall wounds the institution and community we cherish. We believe these policies are a regrettable but necessary response to the state’s actions. While we are committed to doing everything we can to mitigate their effects on the most vulnerable populations of our students and staff, we recognize that many disagree deeply, and that vigorous and vocal protest is an understandable response. The passionate advocacy of students, staff, and faculty for the University and its public mission has been remarkable.

 

Many of the protest activities were appropriate forms of peaceful advocacy. We are concerned, however, about activities at several campuses that disrupted our educational mission and interfered with the freedom of fellow students, faculty, and staff, to teach, learn, research, and work. We are especially concerned about group protests in which a number of individuals attempted to move past police barricades, physically threaten and throw objects at police, and surround vehicles to trap those within. These activities are unlawful and disrespectful of the rights of others, and they create a serious risk of violence for everyone in the area: police, protestors, and bystanders. A number of injuries, some serious, were sustained last week by both protestors and police officers.

 

We will insist, through all avenues open to us, that uses of force by police will be subject to inquiry and review, as well as the policies that govern crowd control. While we expect campus police professionals to be committed to accommodating peaceful protest, we realize that there may be failures of policy or individual action. We are committed to ensuring that the University remains a place where it is safe to teach and learn – and engage in peaceful protest.

 

At the same time, we wish to remind everyone of the limits of protest, and of our obligation to be civil, to show respect for different points of view, and to take personal responsibility for our own and each other’s safety. Occupation of university buildings, for example, directly interferes with the rights of other members of the community.

 

The problems that confront our University are daunting, and finding solutions to them will require the collective best efforts of our students, faculty, staff, and members of the community. Tempers will worsen and patience will shorten as these policies take hold, but we must channel our energies outwards, towards advocating for restoring funding to the University of California so that it can fulfill its mission of providing democratic access to the great research universities of our state.

 

Sincerely,

 

 

Henry C. Powell, Chair

Academic Senate

 

Daniel L. Simmons, Vice Chair

Academic Senate

 

Christopher Kutz, Chair

UC Berkeley Divisional Senate

 

Robert Powell, Chair

UC Davis Divisional Senate

 

Judith Stepan-Norris, Chair

UC Irvine Divisional Senate

 

Robin L. Garrell, Chair

UCLA Divisional Senate

 

Martha Conklin, Chair

UC Merced Divisional Senate

 

Anthony W. Norman, Chair

UC Riverside Divisional Senate

 

William Hodgkiss, Chair

UC San Diego Divisional Senate

 

Elena Fuentes-Afflick, Chair

UC San Francisco Divisional Senate

 

Joel Michaelsen, Chair

UC Santa Barbara Divisional Senate

 

Lori Kletzer, Chair

UC Santa Cruz Divisional Senate

 

Sylvia Hurtado, Chair

Board of Admissions and Relations with Schools

 

Farid Chehab, Chair

Coordinating Committee on Graduate Affairs

 

M. Ines Boechat, Chair

University Committee on Affirmative Action and Diversity

 

Alison Butler, Chair

University Committee on Academic Personnel

 

Keith R. Williams, Chair

University Committee on Educational Policy

 

Shane White, Chair

University Committee on Faculty Welfare

 

Gregory Miller, Chair

University Committee on Research Policy

 

Peter Krapp, Chair

University Committee on Planning and Budget

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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.

——–

Bay Area Biosystematists: 12/8, John Carlos Garza on Genetics & mgmt of California fishes

The Bay Area Biosystematists present:
 
“The use of genetic data to delineate management units for California fishes”

John Carlos Garza
Southwest Fisheries Science Center, NOAA
and
Dept. of Ocean Sciences, UC Santa Cruz

As lead of the Molecular Ecology and Genetic Analysis (MEGA) Team, Dr. Garza and his lab
use population genetic data and analytical techniques to address a broad array of questions in ecology,
evolution, behavior, conservation, and management of marine and anadromous organisms. This talk will focus on identifying management units for California fishes and their relationship to taxonomic units

For more about Dr. Garza’s work, visit his website:
http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=902

Tuesday, December 8th, 2009
At the California Academy of Sciences
Golden Gate Park

Dinner and social hour begin at 5:30 pm              Delicious food!!      Thirst quenching beers and healthy sodas!!

Evening presentation begins at 7:00 pm

RSVP REQUIRED FOR DINNER OR TALK
Please rsvp to Healy Hamilton hhamilton — at —- calacademy.org

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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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NSF looking for grants on "Life in Transition" re:climate change

Just got this email from the National Science Foundation saying that NSF is looking for more grants relating to responses of organisms/ecosystems to climate change.

The Divisions of Integrative Organismal Systems (IOS) and Molecular and Cellular Biosciences (MCB) in the Directorate for Biological Sciences at NSF encourage submission of proposals that address the biochemical, molecular, cellular, genetic and/or organismal underpinnings of adaptation and biological feedbacks to climate change.  Interdisciplinary and systems level approaches to these problems are encouraged. A cross-divisional working group has been established to ensure that exciting proposals in this area receive adequate and appropriate attention. 

Life on earth contributes actively to the forces involved in troposphere climate and chemistry. Not only are organisms key participants in climate and chemistry forcing functions, they are also highly sensitive to changes in many climatic and chemical properties of the troposphere.  Research is needed to understand the limits of biological adjustments to such changes, and the feedbacks on climate and chemistry that will result. 

The Foundation has a rapidly growing commitment to research directed towards understanding the interplay between living organisms and the earth’s climate and surface chemistry.  In the Directorate for Biological Sciences, this was emphasized last year by the establishment of a special Life in Transition activity, as announced in an open letter to the research community, accessible at: http://www.nsf.gov/pubs/2008/nsf08078/nsf08078.jsp?org=NSF.

Please consider submitting proposals of this kind to IOS and MCB using the ‘LiT:’ title preface described in the Life in Transition ‘Dear Colleague’ letter referenced above.  A project summary and introduction that place the proposed  research in the context of global climate change will be most helpful in determining appropriate sources of funding within NSF. 

If you seek further information, queries sent to this return email address will be directed appropriately to insure a prompt reply.

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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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